2024
Journal Articles
Massimo Bellanda; Milena Damulewicz; Barbara Zambelli; Elisa Costanzi; Francesco Gregoris; Stefano Mammi; Silvio C. E. Tosatto; Rodolfo Costa; Giovanni Minervini; Gabriella M. Mazzotta
A PDZ scaffolding/CaM-mediated pathway in Cryptochrome signaling Journal Article
In: Protein Science, vol. 33, no. 3, 2024, ISSN: 09618368, (Cited by: 0).
Abstract | Links:
@article{Bellanda2024,
title = {A PDZ scaffolding/CaM-mediated pathway in Cryptochrome signaling},
author = {Massimo Bellanda and Milena Damulewicz and Barbara Zambelli and Elisa Costanzi and Francesco Gregoris and Stefano Mammi and Silvio C. E. Tosatto and Rodolfo Costa and Giovanni Minervini and Gabriella M. Mazzotta},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85185346556\&doi=10.100%2fpro.4914\&partnerID=40\&md5=9d3ca7169c5c85e7e43289adbe2c3e24},
doi = {10.1002/pro.4914},
issn = {09618368},
year = {2024},
date = {2024-01-01},
journal = {Protein Science},
volume = {33},
number = {3},
publisher = {John Wiley and Sons Inc},
abstract = {Cryptochromes are cardinal constituents of the circadian clock, which orchestrates daily physiological rhythms in living organisms. A growing body of evidence points to their participation in pathways that have not traditionally been associated with circadian clock regulation, implying that cryptochromes may be subject to modulation by multiple signaling mechanisms. In this study, we demonstrate that human CRY2 (hCRY2) forms a complex with the large, modular scaffolding protein known as Multi-PDZ Domain Protein 1 (MUPP1). This interaction is facilitated by the calcium-binding protein Calmodulin (CaM) in a calcium-dependent manner. Our findings suggest a novel cooperative mechanism for the regulation of mammalian cryptochromes, mediated by calcium ions (Ca2+) and CaM. We propose that this Ca2+/CaM-mediated signaling pathway may be an evolutionarily conserved mechanism that has been maintained from Drosophila to mammals, most likely in relation to its potential role in the broader context of cryptochrome function and regulation. Further, the understanding of cryptochrome interactions with other proteins and signaling pathways could lead to a better definition of its role within the intricate network of molecular interactions that govern circadian rhythms. © 2024 The Protein Society.},
note = {Cited by: 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Damiano Piovesan; Davide Zago; Parnal Joshi; M. Clara De Paolis Kaluza; Mahta Mehdiabadi; Rashika Ramola; Alexander Miguel Monzon; Walter Reade; Iddo Friedberg; Predrag Radivojac; Silvio C. E. Tosatto
CAFA-evaluator: a Python tool for benchmarking ontological classification methods Journal Article
In: Bioinformatics Advances, vol. 4, no. 1, 2024, ISSN: 26350041, (Cited by: 2; All Open Access, Gold Open Access).
Abstract | Links:
@article{Piovesan2024,
title = {CAFA-evaluator: a Python tool for benchmarking ontological classification methods},
author = {Damiano Piovesan and Davide Zago and Parnal Joshi and M. Clara De Paolis Kaluza and Mahta Mehdiabadi and Rashika Ramola and Alexander Miguel Monzon and Walter Reade and Iddo Friedberg and Predrag Radivojac and Silvio C. E. Tosatto},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85188993912\&doi=10.109%2fbioad%2fvbae043\&partnerID=40\&md5=b6e09ea188a60708097f5bc31ba115dd},
doi = {10.1093/bioadv/vbae043},
issn = {26350041},
year = {2024},
date = {2024-01-01},
journal = {Bioinformatics Advances},
volume = {4},
number = {1},
publisher = {Oxford University Press},
abstract = {We present CAFA-evaluator, a powerful Python program designed to evaluate the performance of prediction methods on targets with hierarchical concept dependencies. It generalizes multi-label evaluation to modern ontologies where the prediction targets are drawn from a directed acyclic graph and achieves high efficiency by leveraging matrix computation and topological sorting. The program requirements include a small number of standard Python libraries, making CAFA-evaluator easy to maintain. The code replicates the Critical Assessment of protein Function Annotation (CAFA) benchmarking, which evaluates predictions of the consistent subgraphs in Gene Ontology. Owing to its reliability and accuracy, the organizers have selected CAFA-evaluator as the official CAFA evaluation software. © 2024 The Author(s). Published by Oxford University Press.},
note = {Cited by: 2; All Open Access, Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Francesco Gregoris; Giovanni Minervini; Silvio C. E. Tosatto
In Silico Exploration of AHR-HIF Pathway Interplay: Implications for Therapeutic Targeting in ccRCC Journal Article
In: Genes, vol. 15, no. 9, 2024, ISSN: 20734425, (Cited by: 0; All Open Access, Gold Open Access).
Abstract | Links:
@article{Gregoris2024,
title = {In Silico Exploration of AHR-HIF Pathway Interplay: Implications for Therapeutic Targeting in ccRCC},
author = {Francesco Gregoris and Giovanni Minervini and Silvio C. E. Tosatto},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85205114282\&doi=10.339%2fgenes15091167\&partnerID=40\&md5=4358b236c257d898f6c44e2639ebbd9d},
doi = {10.3390/genes15091167},
issn = {20734425},
year = {2024},
date = {2024-01-01},
journal = {Genes},
volume = {15},
number = {9},
publisher = {Multidisciplinary Digital Publishing Institute (MDPI)},
abstract = {The oxygen-sensing pathway is a crucial regulatory circuit that defines cellular conditions and is extensively exploited in cancer development. Pathogenic mutations in the von Hippel\textendashLindau (VHL) tumour suppressor impair its role as a master regulator of hypoxia-inducible factors (HIFs), leading to constitutive HIF activation and uncontrolled angiogenesis, increasing the risk of developing clear cell renal cell carcinoma (ccRCC). HIF hyperactivation can sequester HIF-1β, preventing the aryl hydrocarbon receptor (AHR) from correctly activating gene expression in response to endogenous and exogenous ligands such as TCDD (dioxins). In this study, we used protein\textendashprotein interaction networks and gene expression profiling to characterize the impact of VHL loss on AHR activity. Our findings reveal specific expression patterns of AHR interactors following exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and in ccRCC. We identified several AHR interactors significantly associated with poor survival rates in ccRCC patients. Notably, the upregulation of the androgen receptor (AR) and retinoblastoma-associated protein (RB1) by TCDD, coupled with their respective downregulation in ccRCC and association with poor survival rates, suggests novel therapeutic targets. The strategic activation of the AHR via selective AHR modulators (SAhRMs) could stimulate its anticancer activity, specifically targeting RB1 and AR to reduce cell cycle progression and metastasis formation in ccRCC. Our study provides comprehensive insights into the complex interplay between the AHR and HIF pathways in ccRCC pathogenesis, offering novel strategies for targeted therapeutic interventions. © 2024 by the authors.},
note = {Cited by: 0; All Open Access, Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Ilenia Inciardi; Elena Rizzotto; Francesco Gregoris; Benedetta Fongaro; Alice Sosic; Giovanni Minervini; Patrizia Polverino de Laureto
Catechol-induced covalent modifications modulate the aggregation tendency of α-synuclein: An in-solution and in-silico study Journal Article
In: BioFactors, 2024, ISSN: 09516433, (Cited by: 1).
Abstract | Links:
@article{Inciardi2024,
title = {Catechol-induced covalent modifications modulate the aggregation tendency of α-synuclein: An in-solution and in-silico study},
author = {Ilenia Inciardi and Elena Rizzotto and Francesco Gregoris and Benedetta Fongaro and Alice Sosic and Giovanni Minervini and Patrizia Polverino de Laureto},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85194767977\&doi=10.100%2fbiof.2086\&partnerID=40\&md5=aff1210a238a2481081bf8c704ba8ef5},
doi = {10.1002/biof.2086},
issn = {09516433},
year = {2024},
date = {2024-01-01},
journal = {BioFactors},
publisher = {John Wiley and Sons Inc},
abstract = {Parkinson's disease (PD) stands as a challenging neurodegenerative condition characterized by the emergence of Lewy Bodies (LBs), intracellular inclusions within dopaminergic neurons. These LBs harbor various proteins, prominently including α-Synuclein (Syn) aggregates, implicated in disease pathology. A promising avenue in PD treatment involves targeting Syn aggregation. Recent findings from our research have shown that 3,4-dihydroxyphenylacetic acid (DOPAC) and 3,4-dihydroxyphenylethanol (DOPET) possess the ability to impede the formation of Syn fibrils by disrupting the aggregation process. Notably, these compounds primarily engage in noncovalent interactions with the protein, leading to the formation of off-pathway oligomers that deter fibril growth. Through proteolysis studies and mass spectrometry (MS) analysis, we have identified potential covalent modifications of Syn in the presence of DOPAC, although the exact site remains elusive. Employing molecular dynamics simulations, we delved into how DOPAC-induced covalent alterations might affect the mechanism of Syn aggregation. Our findings indicate that the addition of a covalent adduct on certain residues enhances fibril flexibility without compromising its secondary structure stability. Furthermore, in the monomeric state, the modified residue fosters novel bonding interactions, thereby influencing long-range interactions between the N- and C-termini of the protein. © 2024 International Union of Biochemistry and Molecular Biology.},
note = {Cited by: 1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Alessio Del Conte; Giorgia F Camagni; Damiano Clementel; Giovanni Minervini; Alexander Miguel Monzon; Carlo Ferrari; Damiano Piovesan; Silvio C. E Tosatto
RING 4.0: Faster residue interaction networks with novel interaction types across over 35,000 different chemical structures Journal Article
In: Nucleic Acids Research, vol. 52, no. W1, pp. W306 – W312, 2024, ISSN: 03051048, (Cited by: 5; All Open Access, Gold Open Access).
Abstract | Links:
@article{DelConte2024W306,
title = {RING 4.0: Faster residue interaction networks with novel interaction types across over 35,000 different chemical structures},
author = {Alessio Del Conte and Giorgia F Camagni and Damiano Clementel and Giovanni Minervini and Alexander Miguel Monzon and Carlo Ferrari and Damiano Piovesan and Silvio C. E Tosatto},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85197788039\&doi=10.109%2fna%2fgkae337\&partnerID=40\&md5=bca70d16fbb39f5466a3957673ef9eef},
doi = {10.1093/nar/gkae337},
issn = {03051048},
year = {2024},
date = {2024-01-01},
journal = {Nucleic Acids Research},
volume = {52},
number = {W1},
pages = {W306 \textendash W312},
publisher = {Oxford University Press},
abstract = {Residue interaction networks (RINs) are a valuable approach for representing contacts in protein structures. RINs have been widely used in various research areas, including the analysis of mutation effects, domain-domain communication, catalytic activity, and molecular dynamics simulations. The RING server is a powerful tool to calculate non-covalent molecular interactions based on geometrical parameters, providing high-quality and reliable results. Here, we introduce RING 4.0, which includes significant enhancements for identifying both covalent and non-covalent bonds in protein structures. It now encompasses seven different interaction types, with the addition of π-hydrogen, halogen bonds and metal ion coordination sites. The definitions of all available bond types have also been refined and RING can now process the complete PDB chemical component dictionary (over 35000 different molecules) which provides atom names and covalent connectivity information for all known ligands. Optimization of the software has improved execution time by an order of magnitude. The RING web server has been redesigned to provide a more engaging and interactive user experience, incorporating new visualization tools. Users can now visualize all types of interactions simultaneously in the structure viewer and network component. The web server, including extensive help and tutorials, is available from URL: https://ring.biocomputingup.it/. © 2024 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.},
note = {Cited by: 5; All Open Access, Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Paula Nazarena Arrías; Zarifa Osmanli; Estefanía Peralta; Patricio Manuel Chinestrad; Alexander Miguel Monzon; Silvio C. E. Tosatto
Diversity and structural-functional insights of alpha-solenoid proteins Journal Article
In: Protein Science, vol. 33, no. 11, 2024, ISSN: 09618368, (Cited by: 0; All Open Access, Hybrid Gold Open Access).
Abstract | Links:
@article{Arr\'{i}as2024,
title = {Diversity and structural-functional insights of alpha-solenoid proteins},
author = {Paula Nazarena Arr\'{i}as and Zarifa Osmanli and Estefan\'{i}a Peralta and Patricio Manuel Chinestrad and Alexander Miguel Monzon and Silvio C. E. Tosatto},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85207813713\&doi=10.100%2fpro.5189\&partnerID=40\&md5=846b239a4c9a4105e9b257d05a64e1fb},
doi = {10.1002/pro.5189},
issn = {09618368},
year = {2024},
date = {2024-01-01},
journal = {Protein Science},
volume = {33},
number = {11},
publisher = {John Wiley and Sons Inc},
abstract = {Alpha-solenoids are a significant and diverse subset of structured tandem repeat proteins (STRPs) that are important in various domains of life. This review examines their structural and functional diversity and highlights their role in critical cellular processes such as signaling, apoptosis, and transcriptional regulation. Alpha-solenoids can be classified into three geometric folds: low curvature, high curvature, and corkscrew, as well as eight subfolds: ankyrin repeats; Huntingtin, elongation factor 3, protein phosphatase 2A, and target of rapamycin; armadillo repeats; tetratricopeptide repeats; pentatricopeptide repeats; Pumilio repeats; transcription activator-like; and Sel-1 and Sel-1-like repeats. These subfolds represent distinct protein families with unique structural properties and functions, highlighting the versatility of alpha-solenoids. The review also discusses their association with disease, highlighting their potential as therapeutic targets and their role in protein design. Advances in state-of-the-art structure prediction methods provide new opportunities and challenges in the functional characterization and classification of this kind of fold, emphasizing the need for continued development of methods for their identification and proper data curation and deposition in the main databases. © 2024 The Author(s). Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.},
note = {Cited by: 0; All Open Access, Hybrid Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Shantanu Jain; Constantina Bakolitsa; Steven E. Brenner; Predrag Radivojac; John Moult; Susanna Repo; Roger A. Hoskins; Gaia Andreoletti; Daniel Barsky; Ajithavalli Chellapan; Hoyin Chu; Navya Dabbiru; Naveen K. Kollipara; Melissa Ly; Andrew J. Neumann; Lipika R. Pal; Eric Odell; Gaurav Pandey; Robin C. Peters-Petrulewicz; Rajgopal Srinivasan; Stephen F. Yee; Sri Jyothsna Yeleswarapu; Maya Zuhl; Ogun Adebali; Ayoti Patra; Michael A. Beer; Raghavendra Hosur; Jian Peng; Brady M. Bernard; Michael Berry; Shengcheng Dong; Alan P. Boyle; Aashish Adhikari; Jingqi Chen; Zhiqiang Hu; Robert Wang; Yaqiong Wang; Maximilian Miller; Yanran Wang; Yana Bromberg; Paola Turina; Emidio Capriotti; James J. Han; Kivilcim Ozturk; Hannah Carter; Giulia Babbi; Samuele Bovo; Pietro Di Lena; Pier Luigi Martelli; Castrense Savojardo; Rita Casadio; Melissa S. Cline; Greet De Baets; Sandra Bonache; Orland Díez; Sara Gutiérrez-Enríquez; Alejandro Fernández; Gemma Montalban; Lars Ootes; Selen Özkan; Natàlia Padilla; Casandra Riera; Xavier De la Cruz; Mark Diekhans; Peter J. Huwe; Qiong Wei; Qifang Xu; Roland L. Dunbrack; Valer Gotea; Laura Elnitski; Gennady Margolin; Piero Fariselli; Ivan V. Kulakovskiy; Vsevolod J. Makeev; Dmitry D. Penzar; Ilya E. Vorontsov; Alexander V. Favorov; Julia R. Forman; Marcia Hasenahuer; Maria S. Fornasari; Gustavo Parisi; Ziga Avsec; Muhammed H. Çelik; Thi Yen Duong Nguyen; Julien Gagneur; Fang-Yuan Shi; Matthew D. Edwards; Yuchun Guo; Kevin Tian; Haoyang Zeng; David K. Gifford; Jonathan Göke; Jan Zaucha; Julian Gough; Graham R. S. Ritchie; Adam Frankish; Jonathan M. Mudge; Jennifer Harrow; Erin L. Young; Yao Yu; …
CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods Journal Article
In: Genome Biology, vol. 25, no. 1, 2024, ISSN: 14747596, (Cited by: 11; All Open Access, Gold Open Access).
Abstract | Links:
@article{Jain2024,
title = {CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods},
author = {Shantanu Jain and Constantina Bakolitsa and Steven E. Brenner and Predrag Radivojac and John Moult and Susanna Repo and Roger A. Hoskins and Gaia Andreoletti and Daniel Barsky and Ajithavalli Chellapan and Hoyin Chu and Navya Dabbiru and Naveen K. Kollipara and Melissa Ly and Andrew J. Neumann and Lipika R. Pal and Eric Odell and Gaurav Pandey and Robin C. Peters-Petrulewicz and Rajgopal Srinivasan and Stephen F. Yee and Sri Jyothsna Yeleswarapu and Maya Zuhl and Ogun Adebali and Ayoti Patra and Michael A. Beer and Raghavendra Hosur and Jian Peng and Brady M. Bernard and Michael Berry and Shengcheng Dong and Alan P. Boyle and Aashish Adhikari and Jingqi Chen and Zhiqiang Hu and Robert Wang and Yaqiong Wang and Maximilian Miller and Yanran Wang and Yana Bromberg and Paola Turina and Emidio Capriotti and James J. Han and Kivilcim Ozturk and Hannah Carter and Giulia Babbi and Samuele Bovo and Pietro Di Lena and Pier Luigi Martelli and Castrense Savojardo and Rita Casadio and Melissa S. Cline and Greet De Baets and Sandra Bonache and Orland D\'{i}ez and Sara Guti\'{e}rrez-Enr\'{i}quez and Alejandro Fern\'{a}ndez and Gemma Montalban and Lars Ootes and Selen \"{O}zkan and Nat\`{a}lia Padilla and Casandra Riera and Xavier De la Cruz and Mark Diekhans and Peter J. Huwe and Qiong Wei and Qifang Xu and Roland L. Dunbrack and Valer Gotea and Laura Elnitski and Gennady Margolin and Piero Fariselli and Ivan V. Kulakovskiy and Vsevolod J. Makeev and Dmitry D. Penzar and Ilya E. Vorontsov and Alexander V. Favorov and Julia R. Forman and Marcia Hasenahuer and Maria S. Fornasari and Gustavo Parisi and Ziga Avsec and Muhammed H. \c{C}elik and Thi Yen Duong Nguyen and Julien Gagneur and Fang-Yuan Shi and Matthew D. Edwards and Yuchun Guo and Kevin Tian and Haoyang Zeng and David K. Gifford and Jonathan G\"{o}ke and Jan Zaucha and Julian Gough and Graham R. S. Ritchie and Adam Frankish and Jonathan M. Mudge and Jennifer Harrow and Erin L. Young and Yao Yu and ...},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85187866396\&doi=10.118%2fs13059-023-03113-6\&partnerID=40\&md5=9018a0ff0bf322ce7b902a3f07d71876},
doi = {10.1186/s13059-023-03113-6},
issn = {14747596},
year = {2024},
date = {2024-01-01},
journal = {Genome Biology},
volume = {25},
number = {1},
publisher = {BioMed Central Ltd},
abstract = {Background: The Critical Assessment of Genome Interpretation (CAGI) aims to advance the state-of-the-art for computational prediction of genetic variant impact, particularly where relevant to disease. The five complete editions of the CAGI community experiment comprised 50 challenges, in which participants made blind predictions of phenotypes from genetic data, and these were evaluated by independent assessors. Results: Performance was particularly strong for clinical pathogenic variants, including some difficult-to-diagnose cases, and extends to interpretation of cancer-related variants. Missense variant interpretation methods were able to estimate biochemical effects with increasing accuracy. Assessment of methods for regulatory variants and complex trait disease risk was less definitive and indicates performance potentially suitable for auxiliary use in the clinic. Conclusions: Results show that while current methods are imperfect, they have major utility for research and clinical applications. Emerging methods and increasingly large, robust datasets for training and assessment promise further progress ahead. © The Author(s) 2024.},
note = {Cited by: 11; All Open Access, Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hamidreza Ghafouri; Tamas Lazar; Alessio Del Conte; Luiggi G. Tenorio Ku; Peter Tompa; Silvio C. E. Tosatto; Alexander Miguel Monzon; Maria C. Aspromonte; Pau Bernadó; Belén Chaves-Arquero; Lucia Beatriz Chemes; Damiano Clementel; Tiago N. Cordeiro; Carlos A. Elena-Real; Michael Feig; Isabella C. Felli; Carlo Ferrari; Julie D. Forman-Kay; Tiago Gomes; Frank Gondelaud; Claudiu C. Gradinaru; Tâp Ha-Duong; Teresa Head-Gordon; Pétur O. Heidarsson; Giacomo Janson; Gunnar Jeschke; Emanuela Leonardi; Zi Hao Liu; Sonia Longhi; Xamuel L. Lund; Maria J. Macias; Pau Martin-Malpartida; Davide Mercadante; Assia Mouhand; Gabor Nagy; María Victoria Nugnes; José Manuel Pérez-Cañadillas; Giulia Pesce; Roberta Pierattelli; Damiano Piovesan; Federica Quaglia; Sylvie Ricard-Blum; Paul Robustelli; Amin Sagar; Edoardo Salladini; Lucile Sénicourt; Nathalie Sibille; João M. C. Teixeira; Thomas E. Tsangaris; Mihaly Varadi
PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins Journal Article
In: Nucleic Acids Research, vol. 52, no. D1, pp. D536 – D544, 2024, ISSN: 03051048, (Cited by: 13; All Open Access, Gold Open Access).
Abstract | Links:
@article{Ghafouri2024D536,
title = {PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins},
author = {Hamidreza Ghafouri and Tamas Lazar and Alessio Del Conte and Luiggi G. Tenorio Ku and Peter Tompa and Silvio C. E. Tosatto and Alexander Miguel Monzon and Maria C. Aspromonte and Pau Bernad\'{o} and Bel\'{e}n Chaves-Arquero and Lucia Beatriz Chemes and Damiano Clementel and Tiago N. Cordeiro and Carlos A. Elena-Real and Michael Feig and Isabella C. Felli and Carlo Ferrari and Julie D. Forman-Kay and Tiago Gomes and Frank Gondelaud and Claudiu C. Gradinaru and T\^{a}p Ha-Duong and Teresa Head-Gordon and P\'{e}tur O. Heidarsson and Giacomo Janson and Gunnar Jeschke and Emanuela Leonardi and Zi Hao Liu and Sonia Longhi and Xamuel L. Lund and Maria J. Macias and Pau Martin-Malpartida and Davide Mercadante and Assia Mouhand and Gabor Nagy and Mar\'{i}a Victoria Nugnes and Jos\'{e} Manuel P\'{e}rez-Ca\~{n}adillas and Giulia Pesce and Roberta Pierattelli and Damiano Piovesan and Federica Quaglia and Sylvie Ricard-Blum and Paul Robustelli and Amin Sagar and Edoardo Salladini and Lucile S\'{e}nicourt and Nathalie Sibille and Jo\~{a}o M. C. Teixeira and Thomas E. Tsangaris and Mihaly Varadi},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85181761325\&doi=10.109%2fna%2fgkad947\&partnerID=40\&md5=0ad51562357f3e5f603d744e02f8729a},
doi = {10.1093/nar/gkad947},
issn = {03051048},
year = {2024},
date = {2024-01-01},
journal = {Nucleic Acids Research},
volume = {52},
number = {D1},
pages = {D536 \textendash D544},
publisher = {Oxford University Press},
abstract = {The Protein Ensemble Database (PED) (URL: https://proteinensemble.org) is the primary resource for depositing structural ensembles of intrinsically disordered proteins. This updated version of PED reflects advancements in the field, denoting a continual expansion with a total of 461 entries and 538 ensembles, including those generated without explicit experimental data through novel machine learning (ML) techniques. With this significant increment in the number of ensembles, a few yet-unprecedented new entries entered the database, including those also determined or refined by electron paramagnetic resonance or circular dichroism data. In addition, PED was enriched with several new features, including a novel deposition service, improved user interface, new database cross-referencing options and integration with the 3D-Beacons network\textemdashall representing efforts to improve the FAIRness of the database. Foreseeably, PED will keep growing in size and expanding with new types of ensembles generated by accurate and fast ML-based generative models and coarse-grained simulations. Therefore, among future efforts, priority will be given to further develop the database to be compatible with ensembles modeled at a coarse-grained level. © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.},
note = {Cited by: 13; All Open Access, Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Elisa Granocchio; Luca Andreoli; Santina Magazù; Daniela Sarti; Emanuela Leonardi; Alessandra Murgia; Claudia Ciaccio
Expanding the clinical phenotype of SHANK2-related disorders: childhood apraxia of speech in a patient with a novel SHANK2 pathogenic variant Journal Article
In: European Child and Adolescent Psychiatry, 2024, ISSN: 10188827, (Cited by: 0).
@article{Granocchio2024,
title = {Expanding the clinical phenotype of SHANK2-related disorders: childhood apraxia of speech in a patient with a novel SHANK2 pathogenic variant},
author = {Elisa Granocchio and Luca Andreoli and Santina Magaz\`{u} and Daniela Sarti and Emanuela Leonardi and Alessandra Murgia and Claudia Ciaccio},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85191992890\&doi=10.100%2fs00787-024-02452-4\&partnerID=40\&md5=84b23a23415b79fd91043d1543048c63},
doi = {10.1007/s00787-024-02452-4},
issn = {10188827},
year = {2024},
date = {2024-01-01},
journal = {European Child and Adolescent Psychiatry},
publisher = {Springer Science and Business Media Deutschland GmbH},
note = {Cited by: 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Juan Mac Donagh; Abril Marchesini; Agostina Spiga; Maximiliano José Fallico; Paula Nazarena Arrías; Alexander Miguel Monzon; Aimilia-Christina Vagiona; Mariane Gonçalves-Kulik; Pablo Mier; Miguel A. Andrade-Navarro
Structured Tandem Repeats in Protein Interactions Journal Article
In: International Journal of Molecular Sciences, vol. 25, no. 5, 2024, ISSN: 16616596, (Cited by: 1; All Open Access, Gold Open Access, Green Open Access).
Abstract | Links:
@article{MacDonagh2024,
title = {Structured Tandem Repeats in Protein Interactions},
author = {Juan Mac Donagh and Abril Marchesini and Agostina Spiga and Maximiliano Jos\'{e} Fallico and Paula Nazarena Arr\'{i}as and Alexander Miguel Monzon and Aimilia-Christina Vagiona and Mariane Gon\c{c}alves-Kulik and Pablo Mier and Miguel A. Andrade-Navarro},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85187783312\&doi=10.339%2fijms25052994\&partnerID=40\&md5=36bf2bfc0d625c28b50aab098d0d94e7},
doi = {10.3390/ijms25052994},
issn = {16616596},
year = {2024},
date = {2024-01-01},
journal = {International Journal of Molecular Sciences},
volume = {25},
number = {5},
publisher = {Multidisciplinary Digital Publishing Institute (MDPI)},
abstract = {Tandem repeats (TRs) in protein sequences are consecutive, highly similar sequence motifs. Some types of TRs fold into structural units that pack together in ensembles, forming either an (open) elongated domain or a (closed) propeller, where the last unit of the ensemble packs against the first one. Here, we examine TR proteins (TRPs) to see how their sequence, structure, and evolutionary properties favor them for a function as mediators of protein interactions. Our observations suggest that TRPs bind other proteins using large, structured surfaces like globular domains; in particular, open-structured TR ensembles are favored by flexible termini and the possibility to tightly coil against their targets. While, intuitively, open ensembles of TRs seem prone to evolve due to their potential to accommodate insertions and deletions of units, these evolutionary events are unexpectedly rare, suggesting that they are advantageous for the emergence of the ancestral sequence but are early fixed. We hypothesize that their flexibility makes it easier for further proteins to adapt to interact with them, which would explain their large number of protein interactions. We provide insight into the properties of open TR ensembles, which make them scaffolds for alternative protein complexes to organize genes, RNA and proteins. © 2024 by the authors.},
note = {Cited by: 1; All Open Access, Gold Open Access, Green Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Maria Cristina Aspromonte; Maria Victoria Nugnes; Federica Quaglia; Adel Bouharoua; Silvio C. E. Tosatto; Damiano Piovesan; Vasileios Sagris; Vasilis J. Promponas; Anastasia Chasapi; Erzsébet Fichó; Galo E. Balatti; Gustavo Parisi; Martín González Buitrón; Gabor Erdos; Matyas Pajkos; Zsuzsanna Dosztányi; Laszlo Dobson; Alessio Del Conte; Damiano Clementel; Edoardo Salladini; Emanuela Leonardi; Fatemeh Kordevani; Hamidreza Ghafouri; Luiggi G. Tenorio Ku; Alexander Miguel Monzon; Carlo Ferrari; Zsófia Kálmán; Juliet F. Nilsson; Jaime Santos; Carlos Pintado-Grima; Salvador Ventura; Veronika Ács; Rita Pancsa; Mariane Goncalves Kulik; Miguel A. Andrade-Navarro; Pedro José Barbosa Pereira; Sonia Longhi; Philippe Le Mercier; Julian Bergier; Peter Tompa; Tamas Lazar
DisProt in 2024: improving function annotation of intrinsically disordered proteins Journal Article
In: Nucleic Acids Research, vol. 52, no. D1, pp. D434 – D441, 2024, ISSN: 03051048, (Cited by: 15; All Open Access, Gold Open Access).
Abstract | Links:
@article{Aspromonte2024D434,
title = {DisProt in 2024: improving function annotation of intrinsically disordered proteins},
author = {Maria Cristina Aspromonte and Maria Victoria Nugnes and Federica Quaglia and Adel Bouharoua and Silvio C. E. Tosatto and Damiano Piovesan and Vasileios Sagris and Vasilis J. Promponas and Anastasia Chasapi and Erzs\'{e}bet Fich\'{o} and Galo E. Balatti and Gustavo Parisi and Mart\'{i}n Gonz\'{a}lez Buitr\'{o}n and Gabor Erdos and Matyas Pajkos and Zsuzsanna Doszt\'{a}nyi and Laszlo Dobson and Alessio Del Conte and Damiano Clementel and Edoardo Salladini and Emanuela Leonardi and Fatemeh Kordevani and Hamidreza Ghafouri and Luiggi G. Tenorio Ku and Alexander Miguel Monzon and Carlo Ferrari and Zs\'{o}fia K\'{a}lm\'{a}n and Juliet F. Nilsson and Jaime Santos and Carlos Pintado-Grima and Salvador Ventura and Veronika \'{A}cs and Rita Pancsa and Mariane Goncalves Kulik and Miguel A. Andrade-Navarro and Pedro Jos\'{e} Barbosa Pereira and Sonia Longhi and Philippe Le Mercier and Julian Bergier and Peter Tompa and Tamas Lazar},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85176208048\&doi=10.109%2fna%2fgkad928\&partnerID=40\&md5=fc34ce08667ff42029fdb54d5142c08f},
doi = {10.1093/nar/gkad928},
issn = {03051048},
year = {2024},
date = {2024-01-01},
journal = {Nucleic Acids Research},
volume = {52},
number = {D1},
pages = {D434 \textendash D441},
publisher = {Oxford University Press},
abstract = {DisProt (URL: https://disprot.org) is the gold standard database for intrinsically disordered proteins and regions, providing valuable information about their functions. The latest version of DisProt brings significant advancements, including a broader representation of functions and an enhanced curation process. These improvements aim to increase both the quality of annotations and their coverage at the sequence level. Higher coverage has been achieved by adopting additional evidence codes. Quality of annotations has been improved by systematically applying Minimum Information About Disorder Experiments (MIADE) principles and reporting all the details of the experimental setup that could potentially influence the structural state of a protein. The DisProt database now includes new thematic datasets and has expanded the adoption of Gene Ontology terms, resulting in an extensive functional repertoire which is automatically propagated to UniProtKB. Finally, we show that DisProt’s curated annotations strongly correlate with disorder predictions inferred from AlphaFold2 pLDDT (predicted Local Distance Difference Test) confidence scores. This comparison highlights the utility of DisProt in explaining apparent uncertainty of certain well-defined predicted structures, which often correspond to folding-upon-binding fragments. Overall, DisProt serves as a comprehensive resource, combining experimental evidence of disorder information to enhance our understanding of intrinsically disordered proteins and their functional implications. © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.},
note = {Cited by: 15; All Open Access, Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Federica Quaglia; Anastasia Chasapi; Maria Victoria Nugnes; Maria Cristina Aspromonte; Emanuela Leonardi; Damiano Piovesan; Silvio C. E. Tosatto
Best practices for the manual curation of intrinsically disordered proteins in DisProt Journal Article
In: Database, vol. 2024, 2024, ISSN: 17580463, (Cited by: 1; All Open Access, Gold Open Access).
Abstract | Links:
@article{Quaglia2024,
title = {Best practices for the manual curation of intrinsically disordered proteins in DisProt},
author = {Federica Quaglia and Anastasia Chasapi and Maria Victoria Nugnes and Maria Cristina Aspromonte and Emanuela Leonardi and Damiano Piovesan and Silvio C. E. Tosatto},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85188297172\&doi=10.109%2fdatabas%2fbaae009\&partnerID=40\&md5=df4fca19479789139b3fd19bb35c817f},
doi = {10.1093/database/baae009},
issn = {17580463},
year = {2024},
date = {2024-01-01},
journal = {Database},
volume = {2024},
publisher = {Oxford University Press},
abstract = {The DisProt database is a resource containing manually curated data on experimentally validated intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) from the literature. Developed in 2005, its primary goal was to collect structural and functional information into proteins that lack a fixed three-dimensional structure.Today, DisProt has evolved into a major repository that not only collects experimental data but also contributes to our understanding of the IDPs/IDRs roles in various biological processes, such as autophagy or the life cycle mechanisms in viruses or their involvement in diseases (such as cancer and neurodevelopmental disorders). DisProt offers detailed information on the structural states of IDPs/IDRs, including state transitions, interactions and their functions, all provided as curated annotations. One of the central activities of DisProt is the meticulous curation of experimental data from the literature. For this reason, to ensure that every expert and volunteer curator possesses the requisite knowledge for data evaluation, collection and integration, training courses and curation materials are available. However, biocuration guidelines concur on the importance of developing robust guidelines that not only provide critical information about data consistency but also ensure data acquisition.This guideline aims to provide both biocurators and external users with best practices for manually curating IDPs and IDRs in DisProt. It describes every step of the literature curation process and provides use cases of IDP curation within DisProt. © The Author(s) 2024. Published by Oxford University Press.},
note = {Cited by: 1; All Open Access, Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2023
Journal Articles
Alessio Del Conte; Mahta Mehdiabadi; Adel Bouhraoua; Alexander Miguel Monzon; Silvio C. E. Tosatto; Damiano Piovesan
Critical assessment of protein intrinsic disorder prediction (CAID) – Results of round 2 Journal Article
In: Proteins: Structure, Function and Bioinformatics, vol. 91, no. 12, pp. 1925 – 1934, 2023, ISSN: 08873585, (Cited by: 20; All Open Access, Hybrid Gold Open Access).
Abstract | Links:
@article{Conte20231925,
title = {Critical assessment of protein intrinsic disorder prediction (CAID) - Results of round 2},
author = {Alessio Del Conte and Mahta Mehdiabadi and Adel Bouhraoua and Alexander Miguel Monzon and Silvio C. E. Tosatto and Damiano Piovesan},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85169117009\&doi=10.100%2fprot.26582\&partnerID=40\&md5=20d7d0ec6f796c0901f2a365becf7fa6},
doi = {10.1002/prot.26582},
issn = {08873585},
year = {2023},
date = {2023-01-01},
journal = {Proteins: Structure, Function and Bioinformatics},
volume = {91},
number = {12},
pages = {1925 \textendash 1934},
publisher = {John Wiley and Sons Inc},
abstract = {Protein intrinsic disorder (ID) is a complex and context-dependent phenomenon that covers a continuum between fully disordered states and folded states with long dynamic regions. The lack of a ground truth that fits all ID flavors and the potential for order-to-disorder transitions depending on specific conditions makes ID prediction challenging. The CAID2 challenge aimed to evaluate the performance of different prediction methods across different benchmarks, leveraging the annotation provided by the DisProt database, which stores the coordinates of ID regions when there is experimental evidence in the literature. The CAID2 challenge demonstrated varying performance of different prediction methods across different benchmarks, highlighting the need for continued development of more versatile and efficient prediction software. Depending on the application, researchers may need to balance performance with execution time when selecting a predictor. Methods based on AlphaFold2 seem to be good ID predictors but they are better at detecting absence of order rather than ID regions as defined in DisProt. The CAID2 predictors can be freely used through the CAID Prediction Portal, and CAID has been integrated into OpenEBench, which will become the official platform for running future CAID challenges. © 2023 The Authors. Proteins: Structure, Function, and Bioinformatics published by Wiley Periodicals LLC.},
note = {Cited by: 20; All Open Access, Hybrid Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Damiano Piovesan; Alessio Del Conte; Damiano Clementel; Alexander Miguel Monzon; Martina Bevilacqua; Maria Cristina Aspromonte; Javier A Iserte; Fernando E Orti; Cristina Marino-Buslje; Silvio C. E Tosatto
MobiDB: 10 years of intrinsically disordered proteins Journal Article
In: Nucleic Acids Research, vol. 51, no. 1 D, pp. D438 – D444, 2023, ISSN: 03051048, (Cited by: 61; All Open Access, Gold Open Access, Green Open Access).
Abstract | Links:
@article{Piovesan2023D438,
title = {MobiDB: 10 years of intrinsically disordered proteins},
author = {Damiano Piovesan and Alessio Del Conte and Damiano Clementel and Alexander Miguel Monzon and Martina Bevilacqua and Maria Cristina Aspromonte and Javier A Iserte and Fernando E Orti and Cristina Marino-Buslje and Silvio C. E Tosatto},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85145966264\&doi=10.109%2fna%2fgkac1065\&partnerID=40\&md5=8547b341a7698891915b9e425ab793e7},
doi = {10.1093/nar/gkac1065},
issn = {03051048},
year = {2023},
date = {2023-01-01},
journal = {Nucleic Acids Research},
volume = {51},
number = {1 D},
pages = {D438 \textendash D444},
publisher = {Oxford University Press},
abstract = {The MobiDB database (URL: https://mobidb.org/) is a knowledge base of intrinsically disordered proteins. MobiDB aggregates disorder annotations derived from the literature and from experimental evidence along with predictions for all known protein sequences. MobiDB generates new knowledge and captures the functional significance of disordered regions by processing and combining complementary sources of information. Since its first release 10 years ago, the MobiDB database has evolved in order to improve the quality and coverage of protein disorder annotations and its accessibility. MobiDB has now reached its maturity in terms of data standardization and visualization. Here, we present a new release which focuses on the optimization of user experience and database content. The major advances compared to the previous version are the integration of AlphaFoldDB predictions and the re-implementation of the homology transfer pipeline, which expands manually curated annotations by two orders of magnitude. Finally, the entry page has been restyled in order to provide an overview of the available annotations along with two separate views that highlight structural disorder evidence and functions associated with different binding modes. © 2023 The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.},
note = {Cited by: 61; All Open Access, Gold Open Access, Green Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Eric W. Deutsch; Juan Antonio Vizcaíno; Andrew R. Jones; Pierre-Alain Binz; Henry Lam; Joshua Klein; Wout Bittremieux; Yasset Perez-Riverol; David L. Tabb; Mathias Walzer; Sylvie Ricard-Blum; Henning Hermjakob; Steffen Neumann; Tytus D. Mak; Shin Kawano; Luis Mendoza; Tim Van Den Bossche; Ralf Gabriels; Nuno Bandeira; Jeremy Carver; Benjamin Pullman; Zhi Sun; Nils Hoffmann; Jim Shofstahl; Yunping Zhu; Luana Licata; Federica Quaglia; Silvio C. E. Tosatto; Sandra E. Orchard
Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work Journal Article
In: Journal of Proteome Research, vol. 22, no. 2, pp. 287 – 301, 2023, ISSN: 15353893, (Cited by: 24; All Open Access, Hybrid Gold Open Access).
Abstract | Links:
@article{Deutsch2023287,
title = {Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work},
author = {Eric W. Deutsch and Juan Antonio Vizca\'{i}no and Andrew R. Jones and Pierre-Alain Binz and Henry Lam and Joshua Klein and Wout Bittremieux and Yasset Perez-Riverol and David L. Tabb and Mathias Walzer and Sylvie Ricard-Blum and Henning Hermjakob and Steffen Neumann and Tytus D. Mak and Shin Kawano and Luis Mendoza and Tim Van Den Bossche and Ralf Gabriels and Nuno Bandeira and Jeremy Carver and Benjamin Pullman and Zhi Sun and Nils Hoffmann and Jim Shofstahl and Yunping Zhu and Luana Licata and Federica Quaglia and Silvio C. E. Tosatto and Sandra E. Orchard},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85146633740\&doi=10.102%2facs.jproteome.2c00637\&partnerID=40\&md5=3e3c06dbc2bbe6a80002d31a2e0a7b43},
doi = {10.1021/acs.jproteome.2c00637},
issn = {15353893},
year = {2023},
date = {2023-01-01},
journal = {Journal of Proteome Research},
volume = {22},
number = {2},
pages = {287 \textendash 301},
publisher = {American Chemical Society},
abstract = {The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been successfully developing guidelines, data formats, and controlled vocabularies (CVs) for the proteomics community and other fields supported by mass spectrometry since its inception 20 years ago. Here we describe the general operation of the PSI, including its leadership, working groups, yearly workshops, and the document process by which proposals are thoroughly and publicly reviewed in order to be ratified as PSI standards. We briefly describe the current state of the many existing PSI standards, some of which remain the same as when originally developed, some of which have undergone subsequent revisions, and some of which have become obsolete. Then the set of proposals currently being developed are described, with an open call to the community for participation in the forging of the next generation of standards. Finally, we describe some synergies and collaborations with other organizations and look to the future in how the PSI will continue to promote the open sharing of data and thus accelerate the progress of the field of proteomics. © 2023 The Authors. Published by American Chemical Society.},
note = {Cited by: 24; All Open Access, Hybrid Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Diana Piol; Laura Tosatto; Emanuela Zuccaro; Eric N. Anderson; Antonella Falconieri; Maria J. Polanco; Caterina Marchioretti; Federica Lia; Joseph White; Elisa Bregolin; Giovanni Minervini; Sara Parodi; Xavier Salvatella; Giorgio Arrigoni; Andrea Ballabio; Albert R. La Spada; Silvio C. E. Tosatto; Fabio Sambataro; Diego L. Medina; Udai B. Pandey; Manuela Basso; Maria Pennuto
Antagonistic effect of cyclin-dependent kinases and a calcium-dependent phosphatase on polyglutamine-expanded androgen receptor toxic gain of function Journal Article
In: Science Advances, vol. 9, no. 1, 2023, ISSN: 23752548, (Cited by: 6; All Open Access, Gold Open Access).
Abstract | Links:
@article{Piol2023,
title = {Antagonistic effect of cyclin-dependent kinases and a calcium-dependent phosphatase on polyglutamine-expanded androgen receptor toxic gain of function},
author = {Diana Piol and Laura Tosatto and Emanuela Zuccaro and Eric N. Anderson and Antonella Falconieri and Maria J. Polanco and Caterina Marchioretti and Federica Lia and Joseph White and Elisa Bregolin and Giovanni Minervini and Sara Parodi and Xavier Salvatella and Giorgio Arrigoni and Andrea Ballabio and Albert R. La Spada and Silvio C. E. Tosatto and Fabio Sambataro and Diego L. Medina and Udai B. Pandey and Manuela Basso and Maria Pennuto},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85145870213\&doi=10.112%2fsciadv.ade1694\&partnerID=40\&md5=47b819a09fd41c1bb6bde30c1401e4f7},
doi = {10.1126/sciadv.ade1694},
issn = {23752548},
year = {2023},
date = {2023-01-01},
journal = {Science Advances},
volume = {9},
number = {1},
publisher = {American Association for the Advancement of Science},
abstract = {Spinal and bulbar muscular atrophy is caused by polyglutamine (polyQ) expansions in androgen receptor (AR), generating gain-of-function toxicity that may involve phosphorylation. Using cellular and animal models, we investigated what kinases and phosphatases target polyQ-expanded AR, whether polyQ expansions modify AR phosphorylation, and how this contributes to neurodegeneration. Mass spectrometry showed that polyQ expansions preserve native phosphorylation and increase phosphorylation at conserved sites controlling AR stability and transactivation. In small-molecule screening, we identified that CDC25/CDK2 signaling could enhance AR phosphorylation, and the calcium-sensitive phosphatase calcineurin had opposite effects. Pharmacologic and genetic manipulation of these kinases and phosphatases modified polyQ-expanded AR function and toxicity in cells, flies, and mice. Ablation of CDK2 reduced AR phosphorylation in the brainstem and restored expression of Myc and other genes involved in DNA damage, senescence, and apoptosis, indicating that the cell cycle\textendashregulated kinase plays more than a bystander role in SBMA-vulnerable postmitotic cells. Copyright © 2023 The Authors, some rights reserved;},
note = {Cited by: 6; All Open Access, Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Nahuel Escobedo; Alexander Miguel Monzon; María Silvina Fornasari; Nicolas Palopoli; Gustavo Parisi
Combining Protein Conformational Diversity and Phylogenetic Information Using CoDNaS and CoDNaS-Q Journal Article
In: Current Protocols, vol. 3, no. 5, 2023, ISSN: 26911299, (Cited by: 0; All Open Access, Green Open Access).
Abstract | Links:
@article{Escobedo2023,
title = {Combining Protein Conformational Diversity and Phylogenetic Information Using CoDNaS and CoDNaS-Q},
author = {Nahuel Escobedo and Alexander Miguel Monzon and Mar\'{i}a Silvina Fornasari and Nicolas Palopoli and Gustavo Parisi},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85159198884\&doi=10.100%2fcpz1.764\&partnerID=40\&md5=01fcae4cfec9f15a0d39dfdc6d05c8ab},
doi = {10.1002/cpz1.764},
issn = {26911299},
year = {2023},
date = {2023-01-01},
journal = {Current Protocols},
volume = {3},
number = {5},
publisher = {John Wiley and Sons Inc},
abstract = {CoDNaS (http://ufq.unq.edu.ar/codnas/) and CoDNaS-Q (http://ufq.unq.edu.ar/codnasq) are repositories of proteins with different degrees of conformational diversity. Following the ensemble nature of the native state, conformational diversity represents the structural differences between the conformers in the ensemble. Each entry in CoDNaS and CoDNaS-Q contains a redundant collection of experimentally determined conformers obtained under different conditions. These conformers represent snapshots of the protein dynamism. While CoDNaS contains examples of conformational diversity at the tertiary level, a recent development, CoDNaS-Q, contains examples at the quaternary level. In the emerging age of accurate protein structure prediction by machine learning approaches, many questions remain open regarding the characterization of protein dynamism. In this context, most bioinformatics resources take advantage of distinct features derived from protein alignments, however, the complexity and heterogeneity of information makes it difficult to recover reliable biological signatures. Here we present five protocols to explore tertiary and quaternary conformational diversity at the individual protein level as well as for the characterization of the distribution of conformational diversity at the protein family level in a phylogenetic context. These protocols can provide curated protein families with experimentally known conformational diversity, facilitating the exploration of sequence determinants of protein dynamism. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Assessing conformational diversity with CoDNaS. Alternate Protocol 1: Assessing conformational diversity at the quaternary level with CoDNaS-Q. Basic Protocol 2: Exploring conformational diversity in a protein family. Alternate Protocol 2: Exploring quaternary conformational diversity in a protein family. Basic Protocol 3: Representing conformational diversity in a phylogenetic context. © 2023 Wiley Periodicals LLC.},
note = {Cited by: 0; All Open Access, Green Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Giorgia F. Camagni; Giovanni Minervini; Silvio C. E. Tosatto
Structural Characterization of Hypoxia Inducible Factor α—Prolyl Hydroxylase Domain 2 Interaction through MD Simulations Journal Article
In: International Journal of Molecular Sciences, vol. 24, no. 5, 2023, ISSN: 16616596, (Cited by: 2; All Open Access, Gold Open Access).
Abstract | Links:
@article{Camagni2023,
title = {Structural Characterization of Hypoxia Inducible Factor α\textemdashProlyl Hydroxylase Domain 2 Interaction through MD Simulations},
author = {Giorgia F. Camagni and Giovanni Minervini and Silvio C. E. Tosatto},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85149881431\&doi=10.339%2fijms24054710\&partnerID=40\&md5=90d98f8ae45a38cd27ab4323af8ae2b6},
doi = {10.3390/ijms24054710},
issn = {16616596},
year = {2023},
date = {2023-01-01},
journal = {International Journal of Molecular Sciences},
volume = {24},
number = {5},
publisher = {Multidisciplinary Digital Publishing Institute (MDPI)},
abstract = {The Prolyl Hydroxylases (PHDs) are an enzymatic family that regulates cell oxygen-sensing. PHDs hydroxylate hypoxia-inducible transcription factors α (HIFs-α) driving their proteasomal degradation. Hypoxia inhibits PHDs activity, inducing HIFs-α stabilization and cell adaptation to hypoxia. As a hallmark of cancer, hypoxia promotes neo-angiogenesis and cell proliferation. PHD isoforms are thought to have a variable impact on tumor progression. All isoforms hydroxylate HIF-α (HIF-1,2,3α) with different affinities. However, what determines these differences and how they pair with tumor growth is poorly understood. Here, molecular dynamics simulations were used to characterize the PHD2 binding properties in complexes with HIF-1α and HIF-2α. In parallel, conservation analysis and binding free energy calculations were performed to better understand PHD2 substrate affinity. Our data suggest a direct association between the PHD2 C-terminus and HIF-2α that is not observed in the PHD2/HIF-1α complex. Furthermore, our results indicate that phosphorylation of a PHD2 residue, Thr405, causes a variation in binding energy, despite the fact that this PTM has only a limited structural impact on PHD2/HIFs-α complexes. Collectively, our findings suggest that the PHD2 C-terminus may act as a molecular regulator of PHD’s activity. © 2023 by the authors.},
note = {Cited by: 2; All Open Access, Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Paula Nazarena Arrías; Alexander Miguel Monzon; Damiano Clementel; Soroush Mozaffari; Damiano Piovesan; Andrey V. Kajava; Silvio C. E. Tosatto
The repetitive structure of DNA clamps: An overlooked protein tandem repeat Journal Article
In: Journal of Structural Biology, vol. 215, no. 3, 2023, ISSN: 10478477, (Cited by: 2; All Open Access, Hybrid Gold Open Access).
Abstract | Links:
@article{Arr\'{i}as2023,
title = {The repetitive structure of DNA clamps: An overlooked protein tandem repeat},
author = {Paula Nazarena Arr\'{i}as and Alexander Miguel Monzon and Damiano Clementel and Soroush Mozaffari and Damiano Piovesan and Andrey V. Kajava and Silvio C. E. Tosatto},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85165364940\&doi=10.101%2fj.jsb.2023.108001\&partnerID=40\&md5=a32d9f45912f167f7d63dd4ecf4c4758},
doi = {10.1016/j.jsb.2023.108001},
issn = {10478477},
year = {2023},
date = {2023-01-01},
journal = {Journal of Structural Biology},
volume = {215},
number = {3},
publisher = {Academic Press Inc.},
abstract = {Structured tandem repeats proteins (STRPs) are a specific kind of tandem repeat proteins characterized by a modular and repetitive three-dimensional structure arrangement. The majority of STRPs adopt solenoid structures, but with the increasing availability of experimental structures and high-quality predicted structural models, more STRP folds can be characterized. Here, we describe “Box repeats”, an overlooked STRP fold present in the DNA sliding clamp processivity factors, which has eluded classification although structural data has been available since the late 1990s. Each Box repeat is a β⍺βββ module of about 60 residues, which forms a class V “beads-on-a-string” type STRP. The number of repeats present in processivity factors is organism dependent. Monomers of PCNA proteins in both Archaea and Eukarya have 4 repeats, while the monomers of bacterial beta-sliding clamps have 6 repeats. This new repeat fold has been added to the RepeatsDB database, which now provides structural annotation for 66 Box repeat proteins belonging to different organisms, including viruses. © 2023},
note = {Cited by: 2; All Open Access, Hybrid Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Maria Santa Rocca; Giovanni Minervini; Cinzia Vinanzi; Alberto Bottacin; Federica Lia; Carlo Foresta; Maria Pennuto; Alberto Ferlin
Mutational Screening of Androgen Receptor Gene in 8224 Men of Infertile Couples Journal Article
In: Journal of Clinical Endocrinology and Metabolism, vol. 108, no. 5, pp. 1181 – 1191, 2023, ISSN: 0021972X, (Cited by: 2; All Open Access, Bronze Open Access).
Abstract | Links:
@article{Rocca20231181,
title = {Mutational Screening of Androgen Receptor Gene in 8224 Men of Infertile Couples},
author = {Maria Santa Rocca and Giovanni Minervini and Cinzia Vinanzi and Alberto Bottacin and Federica Lia and Carlo Foresta and Maria Pennuto and Alberto Ferlin},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85152486041\&doi=10.121%2fcline%2fdgac671\&partnerID=40\&md5=b7a9f7deadbf767f38e0f33108febd94},
doi = {10.1210/clinem/dgac671},
issn = {0021972X},
year = {2023},
date = {2023-01-01},
journal = {Journal of Clinical Endocrinology and Metabolism},
volume = {108},
number = {5},
pages = {1181 \textendash 1191},
publisher = {Endocrine Society},
abstract = {Context: Mutations in the androgen receptor (AR) gene might be associated with infertility mainly because they cause various degrees of androgen insensitivity. Objective: The aim of the study was to evaluate the frequency and type of AR variants in a large cohort of infertile males. Methods: A total of 8224 males of Italian idiopathic infertile couples were referred to the University Hospital of Padova. The main outcome measures were mutational screening of AR, computational, and functional analyses. Results: We found 131 patients (1.%) harboring 45 variants in AR gene, of which 18 were novel missense AR variants. Patients with AR gene variants had lower sperm count (P = .048), higher testosterone (T) concentration (P \< .0001), and higher androgen sensitivity index (ASI) (luteinizing hormone × T, P \< .001) than patients without variants. Statistical analyses found T ≥ 15.38 nmol/L and ASI ≥ 180 IU × nmol/L2 as the threshold values to discriminate with good accuracy patients with AR variants. Patients with oligozoospermia and T ≥ 15.38 nmol/L had a 9-fold increased risk of harboring mutations compared with patients with normal sperm count and T \< 15.38 nmol/L (odds ratio 9.29, 9% CI 5.07-17.02). Using computational and functional approaches, we identified 2 novel variants, L595P and L791I, as potentially pathogenic. Conclusion: This is the largest study screening AR gene variants in men of idiopathic infertile couples. We found that the prevalence of variants increased to 3.% in oligozoospermic subjects with T ≥ 15.38 nmol/L. Conversely, more than 8% of men with AR gene variants had low sperm count and high T levels. Based on our findings, we suggest AR sequencing as a routine genetic test in cases of idiopathic oligozoospermia with T ≥ 15.38 nmol/L. © The Author(s) 2022. Published by Oxford University Press on behalf of the Endocrine Society. All rights reserved.},
note = {Cited by: 2; All Open Access, Bronze Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Charlotte Gehin; Museer A. Lone; Winston Lee; Laura Capolupo; Sylvia Ho; Adekemi M. Adeyemi; Erica H. Gerkes; Alexander P. A. Stegmann; Estrella López-Martín; Eva Bermejo-Sánchez; Beatriz Martínez-Delgado; Christiane Zweier; Cornelia Kraus; Bernt Popp; Vincent Strehlow; Daniel Gräfe; Ina Knerr; Eppie R. Jones; Stefano Zamuner; Luciano A. Abriata; Vidya Kunnathully; Brandon E. Moeller; Anthony Vocat; Samuel Rommelaere; Jean-Philippe Bocquete; Evelyne Ruchti; Greta Limoni; Marine Van Campenhoudt; Samuel Bourgeat; Petra Henklein; Christian Gilissen; Bregje W. Bon; Rolph Pfundt; Marjolein H. Willemsen; Jolanda H. Schieving; Emanuela Leonardi; Fiorenza Soli; Alessandra Murgia; Hui Guo; Qiumeng Zhang; Kun Xia; Christina R. Fagerberg; Christoph P. Beier; Martin J. Larsen; Irene Valenzuela; Paula Fernández-Álvarez; Shiyi Xiong; Robert Śmigiel; Vanesa López-González; Lluís Armengol; Manuela Morleo; Angelo Selicorni; Annalaura Torella; Moira Blyth; Nicola S. Cooper; Valerie Wilson; Renske Oegema; Yvan Herenger; Aurore Garde; Ange-Line Bruel; Frederic Tran Mau-Them; Alexis B. R. Maddocks; Jennifer M. Bain; Musadiq A. Bhat; Gregory Costain; Peter Kannu; Ashish Marwaha; Neena L. Champaigne; Michael J. Friez; Ellen B. Richardson; Vykuntaraju K. Gowda; Varunvenkat M. Srinivasan; Yask Gupta; Tze Y. Lim; Simone Sanna-Cherchi; Bruno Lemaitre; Toshiyuki Yamaji; Kentaro Hanada; John E. Burke; Ana Marjia Jakšić; Brian D. McCabe; Paolo De Los Rios; Thorsten Hornemann; Giovanni D’Angelo; Vincenzo A. Gennarino
CERT1 mutations perturb human development by disrupting sphingolipid homeostasis Journal Article
In: Journal of Clinical Investigation, vol. 133, no. 10, 2023, ISSN: 00219738, (Cited by: 11; All Open Access, Gold Open Access).
Abstract | Links:
@article{Gehin2023,
title = {CERT1 mutations perturb human development by disrupting sphingolipid homeostasis},
author = {Charlotte Gehin and Museer A. Lone and Winston Lee and Laura Capolupo and Sylvia Ho and Adekemi M. Adeyemi and Erica H. Gerkes and Alexander P. A. Stegmann and Estrella L\'{o}pez-Mart\'{i}n and Eva Bermejo-S\'{a}nchez and Beatriz Mart\'{i}nez-Delgado and Christiane Zweier and Cornelia Kraus and Bernt Popp and Vincent Strehlow and Daniel Gr\"{a}fe and Ina Knerr and Eppie R. Jones and Stefano Zamuner and Luciano A. Abriata and Vidya Kunnathully and Brandon E. Moeller and Anthony Vocat and Samuel Rommelaere and Jean-Philippe Bocquete and Evelyne Ruchti and Greta Limoni and Marine Van Campenhoudt and Samuel Bourgeat and Petra Henklein and Christian Gilissen and Bregje W. Bon and Rolph Pfundt and Marjolein H. Willemsen and Jolanda H. Schieving and Emanuela Leonardi and Fiorenza Soli and Alessandra Murgia and Hui Guo and Qiumeng Zhang and Kun Xia and Christina R. Fagerberg and Christoph P. Beier and Martin J. Larsen and Irene Valenzuela and Paula Fern\'{a}ndez-\'{A}lvarez and Shiyi Xiong and Robert \'{S}migiel and Vanesa L\'{o}pez-Gonz\'{a}lez and Llu\'{i}s Armengol and Manuela Morleo and Angelo Selicorni and Annalaura Torella and Moira Blyth and Nicola S. Cooper and Valerie Wilson and Renske Oegema and Yvan Herenger and Aurore Garde and Ange-Line Bruel and Frederic Tran Mau-Them and Alexis B. R. Maddocks and Jennifer M. Bain and Musadiq A. Bhat and Gregory Costain and Peter Kannu and Ashish Marwaha and Neena L. Champaigne and Michael J. Friez and Ellen B. Richardson and Vykuntaraju K. Gowda and Varunvenkat M. Srinivasan and Yask Gupta and Tze Y. Lim and Simone Sanna-Cherchi and Bruno Lemaitre and Toshiyuki Yamaji and Kentaro Hanada and John E. Burke and Ana Marjia Jak\v{s}i\'{c} and Brian D. McCabe and Paolo De Los Rios and Thorsten Hornemann and Giovanni D’Angelo and Vincenzo A. Gennarino},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85159733545\&doi=10.117%2fJCI165019\&partnerID=40\&md5=0f32fc96f0219379d9b830efbbbbefb6},
doi = {10.1172/JCI165019},
issn = {00219738},
year = {2023},
date = {2023-01-01},
journal = {Journal of Clinical Investigation},
volume = {133},
number = {10},
publisher = {American Society for Clinical Investigation},
abstract = {Neural differentiation, synaptic transmission, and action potential propagation depend on membrane sphingolipids, whose metabolism is tightly regulated. Mutations in the ceramide transporter CERT (CERT1), which is involved in sphingolipid biosynthesis, are associated with intellectual disability, but the pathogenic mechanism remains obscure. Here, we characterize 31 individuals with de novo missense variants in CERT1. Several variants fall into a previously uncharacterized dimeric helical domain that enables CERT homeostatic inactivation, without which sphingolipid production goes unchecked. The clinical severity reflects the degree to which CERT autoregulation is disrupted, and inhibiting CERT pharmacologically corrects morphological and motor abnormalities in a Drosophila model of the disease, which we call ceramide transporter (CerTra) syndrome. These findings uncover a central role for CERT autoregulation in the control of sphingolipid biosynthetic flux, provide unexpected insight into the structural organization of CERT, and suggest a possible therapeutic approach for patients with CerTra syndrome. © 2023, Gehin et al.},
note = {Cited by: 11; All Open Access, Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Alessio Del Conte; Adel Bouhraoua; Mahta Mehdiabadi; Damiano Clementel; Alexander Miguel Monzon; Silvio C. E. Tosatto; Damiano Piovesan; Alex S. Holehouse; Daniel Griffith; Ryan J. Emenecker; Ashwini Patil; Ronesh Sharma; Tatsuhiko Tsunoda; Alok Sharma; Yi Jun Tang; Bin Liu; Claudio Mirabello; Björn Wallner; Burkhard Rost; Dagmar Ilzhöfer; Maria Littmann; Michael Heinzinger; Lea I. M. Krautheimer; Michael Bernhofer; Liam J. McGuffin; Isabelle Callebaut; Tristan Bitard Feildel; Jian Liu; Jianlin Cheng; Zhiye Guo; Jinbo Xu; Sheng Wang; Nawar Malhis; Jörg Gsponer; Chol-Song Kim; Kun-Sop Han; Myong-Chol Ma; Lukasz Kurgan; Sina Ghadermarzi; Akila Katuwawala; Bi Zhao; Zhenling Peng; Zhonghua Wu; Gang Hu; Kui Wang; Md Tamjidul Hoque; Md Wasi Ul Kabir; Michele Vendruscolo; Pietro Sormanni; Min Li; Fuhao Zhang; Pengzhen Jia; Yida Wang; Michail Yu Lobanov; Oxana V. Galzitskaya; Wim Vranken; Adrián Díaz; Thomas Litfin; Yaoqi Zhou; Jack Hanson; Kuldip Paliwal; Zsuzsanna Dosztányi; Gábor Erdős
CAID prediction portal: A comprehensive service for predicting intrinsic disorder and binding regions in proteins Journal Article
In: Nucleic Acids Research, vol. 51, no. W1, pp. W62 – W69, 2023, ISSN: 03051048, (Cited by: 16; All Open Access, Gold Open Access).
Abstract | Links:
@article{DelConte2023W62,
title = {CAID prediction portal: A comprehensive service for predicting intrinsic disorder and binding regions in proteins},
author = {Alessio Del Conte and Adel Bouhraoua and Mahta Mehdiabadi and Damiano Clementel and Alexander Miguel Monzon and Silvio C. E. Tosatto and Damiano Piovesan and Alex S. Holehouse and Daniel Griffith and Ryan J. Emenecker and Ashwini Patil and Ronesh Sharma and Tatsuhiko Tsunoda and Alok Sharma and Yi Jun Tang and Bin Liu and Claudio Mirabello and Bj\"{o}rn Wallner and Burkhard Rost and Dagmar Ilzh\"{o}fer and Maria Littmann and Michael Heinzinger and Lea I. M. Krautheimer and Michael Bernhofer and Liam J. McGuffin and Isabelle Callebaut and Tristan Bitard Feildel and Jian Liu and Jianlin Cheng and Zhiye Guo and Jinbo Xu and Sheng Wang and Nawar Malhis and J\"{o}rg Gsponer and Chol-Song Kim and Kun-Sop Han and Myong-Chol Ma and Lukasz Kurgan and Sina Ghadermarzi and Akila Katuwawala and Bi Zhao and Zhenling Peng and Zhonghua Wu and Gang Hu and Kui Wang and Md Tamjidul Hoque and Md Wasi Ul Kabir and Michele Vendruscolo and Pietro Sormanni and Min Li and Fuhao Zhang and Pengzhen Jia and Yida Wang and Michail Yu Lobanov and Oxana V. Galzitskaya and Wim Vranken and Adri\'{a}n D\'{i}az and Thomas Litfin and Yaoqi Zhou and Jack Hanson and Kuldip Paliwal and Zsuzsanna Doszt\'{a}nyi and G\'{a}bor Erd\H{o}s},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85163958831\&doi=10.109%2fna%2fgkad430\&partnerID=40\&md5=a458ba56037429c6a042f7610f3cb4bf},
doi = {10.1093/nar/gkad430},
issn = {03051048},
year = {2023},
date = {2023-01-01},
journal = {Nucleic Acids Research},
volume = {51},
number = {W1},
pages = {W62 \textendash W69},
publisher = {Oxford University Press},
abstract = {Intrinsic disorder (ID) in proteins is well-established in structural biology, with increasing evidence for its involvement in essential biological processes. As measuring dynamic ID behavior experimentally on a large scale remains difficult, scores of published ID predictors have tried to fill this gap. Unfortunately, their heterogeneity makes it difficult to compare performance, confounding biologists wanting to make an informed choice. To address this issue, the Critical Assessment of protein Intrinsic Disorder (CAID) benchmarks predictors for ID and binding regions as a community blind-test in a standardized computing environment. Here we present the CAID Prediction Portal, a web server executing all CAID methods on user-defined sequences. The server generates standardized output and facilitates comparison between methods, producing a consensus prediction highlighting high-confidence ID regions. The website contains extensive documentation explaining the meaning of different CAID statistics and providing a brief description of all methods. Predictor output is visualized in an interactive feature viewer and made available for download in a single table, with the option to recover previous sessions via a private dashboard. The CAID Prediction Portal is a valuable resource for researchers interested in studying ID in proteins. The server is available at the URL: https://caid.idpcentral.org. © 2023 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.},
note = {Cited by: 16; All Open Access, Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Bálint Mészáros; András Hatos; Nicolas Palopoli; Federica Quaglia; Edoardo Salladini; Kim Van Roey; Haribabu Arthanari; Zsuzsanna Dosztányi; Isabella C. Felli; Patrick D. Fischer; Jeffrey C. Hoch; Cy M. Jeffries; Sonia Longhi; Emiliano Maiani; Sandra Orchard; Rita Pancsa; Elena Papaleo; Roberta Pierattelli; Damiano Piovesan; Iva Pritisanac; Luiggi Tenorio; Thibault Viennet; Peter Tompa; Wim Vranken; Silvio C. E. Tosatto; Norman E. Davey
Minimum information guidelines for experiments structurally characterizing intrinsically disordered protein regions Journal Article
In: Nature Methods, vol. 20, no. 9, pp. 1291 – 1303, 2023, ISSN: 15487091, (Cited by: 7; All Open Access, Bronze Open Access, Green Open Access).
Abstract | Links:
@article{M\'{e}sz\'{a}ros20231291,
title = {Minimum information guidelines for experiments structurally characterizing intrinsically disordered protein regions},
author = {B\'{a}lint M\'{e}sz\'{a}ros and Andr\'{a}s Hatos and Nicolas Palopoli and Federica Quaglia and Edoardo Salladini and Kim Van Roey and Haribabu Arthanari and Zsuzsanna Doszt\'{a}nyi and Isabella C. Felli and Patrick D. Fischer and Jeffrey C. Hoch and Cy M. Jeffries and Sonia Longhi and Emiliano Maiani and Sandra Orchard and Rita Pancsa and Elena Papaleo and Roberta Pierattelli and Damiano Piovesan and Iva Pritisanac and Luiggi Tenorio and Thibault Viennet and Peter Tompa and Wim Vranken and Silvio C. E. Tosatto and Norman E. Davey},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85164196588\&doi=10.103%2fs41592-023-01915-x\&partnerID=40\&md5=af65986826866a6ce2801c43a3d9d29a},
doi = {10.1038/s41592-023-01915-x},
issn = {15487091},
year = {2023},
date = {2023-01-01},
journal = {Nature Methods},
volume = {20},
number = {9},
pages = {1291 \textendash 1303},
publisher = {Nature Research},
abstract = {An unambiguous description of an experiment, and the subsequent biological observation, is vital for accurate data interpretation. Minimum information guidelines define the fundamental complement of data that can support an unambiguous conclusion based on experimental observations. We present the Minimum Information About Disorder Experiments (MIADE) guidelines to define the parameters required for the wider scientific community to understand the findings of an experiment studying the structural properties of intrinsically disordered regions (IDRs). MIADE guidelines provide recommendations for data producers to describe the results of their experiments at source, for curators to annotate experimental data to community resources and for database developers maintaining community resources to disseminate the data. The MIADE guidelines will improve the interpretability of experimental results for data consumers, facilitate direct data submission, simplify data curation, improve data exchange among repositories and standardize the dissemination of the key metadata on an IDR experiment by IDR data sources. © 2023, Springer Nature America, Inc.},
note = {Cited by: 7; All Open Access, Bronze Open Access, Green Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Andras Hatos; João M. C Teixeira; Susana Barrera-Vilarmau; Attila Horvath; Silvio C. E Tosatto; Michele Vendruscolo; Monika Fuxreiter
FuzPred: A web server for the sequence-based prediction of the context-dependent binding modes of proteins Journal Article
In: Nucleic Acids Research, vol. 51, no. W1, pp. W198 – W206, 2023, ISSN: 03051048, (Cited by: 8; All Open Access, Gold Open Access).
Abstract | Links:
@article{Hatos2023W198,
title = {FuzPred: A web server for the sequence-based prediction of the context-dependent binding modes of proteins},
author = {Andras Hatos and Jo\~{a}o M. C Teixeira and Susana Barrera-Vilarmau and Attila Horvath and Silvio C. E Tosatto and Michele Vendruscolo and Monika Fuxreiter},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85164245294\&doi=10.109%2fna%2fgkad214\&partnerID=40\&md5=732e97008f88abbbfa755ec7a4fa1ee6},
doi = {10.1093/nar/gkad214},
issn = {03051048},
year = {2023},
date = {2023-01-01},
journal = {Nucleic Acids Research},
volume = {51},
number = {W1},
pages = {W198 \textendash W206},
publisher = {Oxford University Press},
abstract = {Proteins form complex interactions in the cellular environment to carry out their functions. They exhibit a wide range of binding modes depending on the cellular conditions, which result in a variety of ordered or disordered assemblies. To help rationalise the binding behavior of proteins, the FuzPred server predicts their sequence-based binding modes without specifying their binding partners. The binding mode defines whether the bound state is formed through a disorder-To-order transition resulting in a well-defined conformation, or through a disorder-To-disorder transition where the binding partners remain conformationally heterogeneous. To account for the context-dependent nature of the binding modes, the FuzPred method also estimates the multiplicity of binding modes, the likelihood of sampling multiple binding modes. Protein regions with a high multiplicity of binding modes may serve as regulatory sites or hot-spots for structural transitions in the assembly. To facilitate the interpretation of the predictions, protein regions with different interaction behaviors can be visualised on protein structures generated by AlphaFold. The FuzPred web server (https://fuzpred.bio.unipd.it) thus offers insights into the structural and dynamical changes of proteins upon interactions and contributes to development of structure-function relationships under a variety of cellular conditions. © 2023 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.},
note = {Cited by: 8; All Open Access, Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Niels Vos; Jack Reilly; Mariet W Elting; Philippe M Campeau; David Coman; Zornitza Stark; Tiong Yang Tan; David J Amor; Simran Kaur; Miya Stjohn; Angela T Morgan; Benjamin A Kamien; Chirag Patel; Matthew L Tedder; Giuseppe Merla; Paolo Prontera; Marco Castori; Kai Muru; Felicity Collins; John Christodoulou; Janine Smith; Bruria Ben Zeev; Alessandra Murgia; Emanuela Leonardi; Natacha Esber; Antonio Martinez-Monseny; Didac Casas-Alba; Matthew Wallis; Marcel Mannens; Michael A Levy; Raissa Relator; Marielle Alders; Bekim Sadikovic
DNA methylation episignatures are sensitive and specific biomarkers for detection of patients with KAT6A/KAT6B variants Journal Article
In: Epigenomics, vol. 15, no. 6, pp. 351 – 367, 2023, ISSN: 17501911, (Cited by: 3).
Abstract | Links:
@article{Vos2023351,
title = {DNA methylation episignatures are sensitive and specific biomarkers for detection of patients with KAT6A/KAT6B variants},
author = {Niels Vos and Jack Reilly and Mariet W Elting and Philippe M Campeau and David Coman and Zornitza Stark and Tiong Yang Tan and David J Amor and Simran Kaur and Miya Stjohn and Angela T Morgan and Benjamin A Kamien and Chirag Patel and Matthew L Tedder and Giuseppe Merla and Paolo Prontera and Marco Castori and Kai Muru and Felicity Collins and John Christodoulou and Janine Smith and Bruria Ben Zeev and Alessandra Murgia and Emanuela Leonardi and Natacha Esber and Antonio Martinez-Monseny and Didac Casas-Alba and Matthew Wallis and Marcel Mannens and Michael A Levy and Raissa Relator and Marielle Alders and Bekim Sadikovic},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85160965403\&doi=10.221%2fepi-2023-0079\&partnerID=40\&md5=5fb586acb83064545e1a62385bf47b83},
doi = {10.2217/epi-2023-0079},
issn = {17501911},
year = {2023},
date = {2023-01-01},
journal = {Epigenomics},
volume = {15},
number = {6},
pages = {351 \textendash 367},
publisher = {Newlands Press Ltd},
abstract = {Accurate diagnosis for patients living with neurodevelopmental disorders is often met with numerous challenges, related to the ambiguity of findings and lack of specificity in genetic variants leading to pathology. Genome-wide DNA methylation analysis has been used to develop highly sensitive and specific 'episignatures' as biomarkers capable of differentiating and classifying complex neurodevelopmental disorders. In this study we describe distinct episignatures for KAT6A syndrome, caused by pathogenic variants in the lysine acetyltransferase A gene (KAT6A), and for the two neurodevelopmental disorders associated with lysine acetyl transferase B (KAT6B). We demonstrate the ability of our models to differentiate between highly overlapping episignatures, increasing the ability to effectively identify and diagnose these conditions. © 2023 Future Medicine Ltd.},
note = {Cited by: 3},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Suzi A. Aleksander; James Balhoff; Seth Carbon; J. Michael Cherry; Harold J. Drabkin; Dustin Ebert; Marc Feuermann; Pascale Gaudet; Nomi L. Harris; David P. Hill; Raymond Lee; Huaiyu Mi; Sierra Moxon; Christopher J. Mungall; Anushya Muruganugan; Tremayne Mushayahama; Paul W. Sternberg; Paul D. Thomas; Kimberly Van Auken; Jolene Ramsey; Deborah A. Siegele; Rex L. Chisholm; Petra Fey; Maria Cristina Aspromonte; Maria Victoria Nugnes; Federica Quaglia; Silvio Tosatto; Michelle Giglio; Suvarna Nadendla; Giulia Antonazzo; Helen Attrill; Gil Dos Santos; Steven Marygold; Victor Strelets; Christopher J. Tabone; Jim Thurmond; Pinglei Zhou; Saadullah H. Ahmed; Praoparn Asanitthong; Diana Luna Buitrago; Meltem N. Erdol; Matthew C. Gage; Mohamed Ali Kadhum; Kan Yan Chloe Li; Miao Long; Aleksandra Michalak; Angeline Pesala; Armalya Pritazahra; Shirin C. C. Saverimuttu; Renzhi Su; Kate E. Thurlow; Ruth C Lovering; Colin Logie; Snezhana Oliferenko; Judith Blake; Karen Christie; Lori Corbani; Mary E. Dolan; Li Ni; Dmitry Sitnikov; Cynthia Smith; Alayne Cuzick; James Seager; Laurel Cooper; Justin Elser; Pankaj Jaiswal; Parul Gupta; Sushma Naithani; Manuel Lera-Ramirez; Kim Rutherford; Valerie Wood; Jeffrey L. De Pons; Melinda R. Dwinell; G. Thomas Hayman; Mary L. Kaldunski; Anne E. Kwitek; Stanley J. F. Laulederkind; Marek A. Tutaj; Mahima Vedi; Shur-Jen Wang; Peter D’Eustachio; Lucila Aimo; Kristian Axelsen; Alan Bridge; Nevila Hyka-Nouspikel; Anne Morgat; Stacia R. Engel; Kalpana Karra; Stuart R. Miyasato; Robert S. Nash; Marek S. Skrzypek; Shuai Weng; Edith D. Wong; Erika Bakker; Tanya Z. Berardini; Leonore Reiser; Andrea Auchincloss; Ghislaine Argoud-Puy; Marie-Claude Blatter; Emmanuel Boutet; …
The Gene Ontology knowledgebase in 2023 Journal Article
In: Genetics, vol. 224, no. 1, 2023, ISSN: 00166731, (Cited by: 570; All Open Access, Hybrid Gold Open Access).
Abstract | Links:
@article{Aleksander2023,
title = {The Gene Ontology knowledgebase in 2023},
author = {Suzi A. Aleksander and James Balhoff and Seth Carbon and J. Michael Cherry and Harold J. Drabkin and Dustin Ebert and Marc Feuermann and Pascale Gaudet and Nomi L. Harris and David P. Hill and Raymond Lee and Huaiyu Mi and Sierra Moxon and Christopher J. Mungall and Anushya Muruganugan and Tremayne Mushayahama and Paul W. Sternberg and Paul D. Thomas and Kimberly Van Auken and Jolene Ramsey and Deborah A. Siegele and Rex L. Chisholm and Petra Fey and Maria Cristina Aspromonte and Maria Victoria Nugnes and Federica Quaglia and Silvio Tosatto and Michelle Giglio and Suvarna Nadendla and Giulia Antonazzo and Helen Attrill and Gil Dos Santos and Steven Marygold and Victor Strelets and Christopher J. Tabone and Jim Thurmond and Pinglei Zhou and Saadullah H. Ahmed and Praoparn Asanitthong and Diana Luna Buitrago and Meltem N. Erdol and Matthew C. Gage and Mohamed Ali Kadhum and Kan Yan Chloe Li and Miao Long and Aleksandra Michalak and Angeline Pesala and Armalya Pritazahra and Shirin C. C. Saverimuttu and Renzhi Su and Kate E. Thurlow and Ruth C Lovering and Colin Logie and Snezhana Oliferenko and Judith Blake and Karen Christie and Lori Corbani and Mary E. Dolan and Li Ni and Dmitry Sitnikov and Cynthia Smith and Alayne Cuzick and James Seager and Laurel Cooper and Justin Elser and Pankaj Jaiswal and Parul Gupta and Sushma Naithani and Manuel Lera-Ramirez and Kim Rutherford and Valerie Wood and Jeffrey L. De Pons and Melinda R. Dwinell and G. Thomas Hayman and Mary L. Kaldunski and Anne E. Kwitek and Stanley J. F. Laulederkind and Marek A. Tutaj and Mahima Vedi and Shur-Jen Wang and Peter D'Eustachio and Lucila Aimo and Kristian Axelsen and Alan Bridge and Nevila Hyka-Nouspikel and Anne Morgat and Stacia R. Engel and Kalpana Karra and Stuart R. Miyasato and Robert S. Nash and Marek S. Skrzypek and Shuai Weng and Edith D. Wong and Erika Bakker and Tanya Z. Berardini and Leonore Reiser and Andrea Auchincloss and Ghislaine Argoud-Puy and Marie-Claude Blatter and Emmanuel Boutet and ...},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85164785564\&doi=10.109%2fgenetic%2fiyad031\&partnerID=40\&md5=d315a8c84634510d971d9d805f26769d},
doi = {10.1093/genetics/iyad031},
issn = {00166731},
year = {2023},
date = {2023-01-01},
journal = {Genetics},
volume = {224},
number = {1},
publisher = {Oxford University Press},
abstract = {The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO - a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations - evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs) - mechanistic models of molecular "pathways"(GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project. © 2023 The Author(s). Published by Oxford University Press on behalf of The Genetics Society of America.},
note = {Cited by: 570; All Open Access, Hybrid Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Alexander Miguel Monzon; Paula Nazarena Arrías; Arne Elofsson; Pablo Mier; Miguel A. Andrade-Navarro; Martina Bevilacqua; Damiano Clementel; Alex Bateman; Layla Hirsh; Maria Silvina Fornasari; Gustavo Parisi; Damiano Piovesan; Andrey V. Kajava; Silvio C. E. Tosatto
A STRP-ed definition of Structured Tandem Repeats in Proteins Journal Article
In: Journal of Structural Biology, vol. 215, no. 4, 2023, ISSN: 10478477, (Cited by: 3; All Open Access, Hybrid Gold Open Access).
Abstract | Links:
@article{Monzon2023,
title = {A STRP-ed definition of Structured Tandem Repeats in Proteins},
author = {Alexander Miguel Monzon and Paula Nazarena Arr\'{i}as and Arne Elofsson and Pablo Mier and Miguel A. Andrade-Navarro and Martina Bevilacqua and Damiano Clementel and Alex Bateman and Layla Hirsh and Maria Silvina Fornasari and Gustavo Parisi and Damiano Piovesan and Andrey V. Kajava and Silvio C. E. Tosatto},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85169818438\&doi=10.101%2fj.jsb.2023.108023\&partnerID=40\&md5=193df29b5c5687ec816f2b9142ae876a},
doi = {10.1016/j.jsb.2023.108023},
issn = {10478477},
year = {2023},
date = {2023-01-01},
journal = {Journal of Structural Biology},
volume = {215},
number = {4},
publisher = {Academic Press Inc.},
abstract = {Tandem Repeat Proteins (TRPs) are a class of proteins with repetitive amino acid sequences that have been studied extensively for over two decades. Different features at the level of sequence, structure, function and evolution have been attributed to them by various authors. And yet many of its salient features appear only when looking at specific subclasses of protein tandem repeats. Here, we attempt to rationalize the existing knowledge on Tandem Repeat Proteins (TRPs) by pointing out several dichotomies. The emerging picture is more nuanced than generally assumed and allows us to draw some boundaries of what is not a “proper” TRP. We conclude with an operational definition of a specific subset, which we have denominated STRPs (Structural Tandem Repeat Proteins), which separates a subclass of tandem repeats with distinctive features from several other less well-defined types of repeats. We believe that this definition will help researchers in the field to better characterize the biological meaning of this large yet largely understudied group of proteins. © 2023},
note = {Cited by: 3; All Open Access, Hybrid Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Alessio Del Conte; Alexander Miguel Monzon; Damiano Clementel; Giorgia F. Camagni; Giovanni Minervini; Silvio C. E. Tosatto; Damiano Piovesan
RING-PyMOL: residue interaction networks of structural ensembles and molecular dynamics Journal Article
In: Bioinformatics, vol. 39, no. 5, 2023, ISSN: 13674803, (Cited by: 8; All Open Access, Gold Open Access, Green Open Access).
Abstract | Links:
@article{DelConte2023,
title = {RING-PyMOL: residue interaction networks of structural ensembles and molecular dynamics},
author = {Alessio Del Conte and Alexander Miguel Monzon and Damiano Clementel and Giorgia F. Camagni and Giovanni Minervini and Silvio C. E. Tosatto and Damiano Piovesan},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85159553803\&doi=10.109%2fbioinformatic%2fbtad260\&partnerID=40\&md5=39b2bf96d22ea0ee520b95f47b590984},
doi = {10.1093/bioinformatics/btad260},
issn = {13674803},
year = {2023},
date = {2023-01-01},
journal = {Bioinformatics},
volume = {39},
number = {5},
publisher = {Oxford University Press},
abstract = {RING-PyMOL is a plugin for PyMOL providing a set of analysis tools for structural ensembles and molecular dynamic simulations. RING-PyMOL combines residue interaction networks, as provided by the RING software, with structural clustering to enhance the analysis and visualization of the conformational complexity. It combines precise calculation of non-covalent interactions with the power of PyMOL to manipulate and visualize protein structures. The plugin identifies and highlights correlating contacts and interaction patterns that can explain structural allostery, active sites, and structural heterogeneity connected with molecular function. It is easy to use and extremely fast, processing and rendering hundreds of models and long trajectories in seconds. RING-PyMOL generates a number of interactive plots and output files for use with external tools. The underlying RING software has been improved extensively. It is 10 times faster, can process mmCIF files and it identifies typed interactions also for nucleic acids. © The Author(s) 2023. Published by Oxford University Press.},
note = {Cited by: 8; All Open Access, Gold Open Access, Green Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Emanuela Leonardi; Maria Cristina Aspromonte; Denise Drongitis; Elisa Bettella; Lucia Verrillo; Roberta Polli; Meriel McEntagart; Laura Licchetta; Robertino Dilena; Stefano D’Arrigo; Claudia Ciaccio; Silvia Esposito; Vincenzo Leuzzi; Annalaura Torella; Demetrio Baldo; Fortunato Lonardo; Giulia Bonato; Serena Pellegrin; Franco Stanzial; Renata Posmyk; Ewa Kaczorowska; Miryam Carecchio; Monika Gos; Sylwia Rzońca-Niewczas; Maria Giuseppina Miano; Alessandra Murgia
Expanding the genetics and phenotypic spectrum of Lysine-specific demethylase 5C (KDM5C): a report of 13 novel variants Journal Article
In: European Journal of Human Genetics, vol. 31, no. 2, pp. 202 – 215, 2023, ISSN: 10184813, (Cited by: 5; All Open Access, Green Open Access).
Abstract | Links:
@article{Leonardi2023202,
title = {Expanding the genetics and phenotypic spectrum of Lysine-specific demethylase 5C (KDM5C): a report of 13 novel variants},
author = {Emanuela Leonardi and Maria Cristina Aspromonte and Denise Drongitis and Elisa Bettella and Lucia Verrillo and Roberta Polli and Meriel McEntagart and Laura Licchetta and Robertino Dilena and Stefano D’Arrigo and Claudia Ciaccio and Silvia Esposito and Vincenzo Leuzzi and Annalaura Torella and Demetrio Baldo and Fortunato Lonardo and Giulia Bonato and Serena Pellegrin and Franco Stanzial and Renata Posmyk and Ewa Kaczorowska and Miryam Carecchio and Monika Gos and Sylwia Rzo\'{n}ca-Niewczas and Maria Giuseppina Miano and Alessandra Murgia},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85142646250\&doi=10.103%2fs41431-022-01233-4\&partnerID=40\&md5=56692e2c9b3994a0703776134808e698},
doi = {10.1038/s41431-022-01233-4},
issn = {10184813},
year = {2023},
date = {2023-01-01},
journal = {European Journal of Human Genetics},
volume = {31},
number = {2},
pages = {202 \textendash 215},
publisher = {Springer Nature},
abstract = {Lysine-specific demethylase 5C (KDM5C) has been identified as an important chromatin remodeling gene, contributing to X-linked neurodevelopmental disorders (NDDs). The KDM5C gene, located in the Xp22 chromosomal region, encodes the H3K4me3-me2 eraser involved in neuronal plasticity and dendritic growth. Here we report 30 individuals carrying 13 novel and one previously identified KDM5C variants. Our cohort includes the first reported case of somatic mosaicism in a male carrying a KDM5C nucleotide substitution, and a dual molecular finding in a female carrying a homozygous truncating FUCA1 alteration together with a de novo KDM5C variant. With the use of next generation sequencing strategies, we detected 1 frameshift, 1 stop codon, 2 splice-site and 10 missense variants, which pathogenic role was carefully investigated by a thorough bioinformatic analysis. The pattern of X-chromosome inactivation was found to have an impact on KDM5C phenotypic expression in females of our cohort. The affected individuals of our case series manifested a neurodevelopmental condition characterized by psychomotor delay, intellectual disability with speech disorders, and behavioral features with particular disturbed sleep pattern; other observed clinical manifestations were short stature, obesity and hypertrichosis. Collectively, these findings expand the current knowledge about the pathogenic mechanisms leading to dysfunction of this important chromatin remodeling gene and contribute to a refinement of the KDM5C phenotypic spectrum. © 2022, This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.},
note = {Cited by: 5; All Open Access, Green Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Elizabeth Martínez-Pérez; Mátyás Pajkos; Silvio C. E. Tosatto; Toby J. Gibson; Zsuzsanna Dosztanyi; Cristina Marino-Buslje
Pipeline for transferring annotations between proteins beyond globular domains Journal Article
In: Protein Science, vol. 32, no. 7, 2023, ISSN: 09618368, (Cited by: 2; All Open Access, Hybrid Gold Open Access).
Abstract | Links:
@article{Mart\'{i}nez-P\'{e}rez2023,
title = {Pipeline for transferring annotations between proteins beyond globular domains},
author = {Elizabeth Mart\'{i}nez-P\'{e}rez and M\'{a}ty\'{a}s Pajkos and Silvio C. E. Tosatto and Toby J. Gibson and Zsuzsanna Dosztanyi and Cristina Marino-Buslje},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85163371698\&doi=10.100%2fpro.4655\&partnerID=40\&md5=8bb4b0ffc634a32f0fc5fdf14ab4245f},
doi = {10.1002/pro.4655},
issn = {09618368},
year = {2023},
date = {2023-01-01},
journal = {Protein Science},
volume = {32},
number = {7},
publisher = {John Wiley and Sons Inc},
abstract = {DisProt is the primary repository of Intrinsically Disordered Proteins (IDPs). This database is manually curated and the annotations there have strong experimental support. Currently, DisProt contains a relatively small number of proteins highlighting the importance of transferring annotations regarding verified disorder state and corresponding functions to homologous proteins in other species. In such a way, providing them with highly valuable information to better understand their biological roles. While the principles and practicalities of homology transfer are well-established for globular proteins, these are largely lacking for disordered proteins. We used DisProt to evaluate the transferability of the annotation terms to orthologous proteins. For each protein, we looked for their orthologs, with the assumption that they will have a similar function. Then, for each protein and their orthologs, we made multiple sequence alignments (MSAs). Disordered sequences are fast evolving and can be hard to align, therefore, we implemented alignment quality control steps ensuring robust alignments before mapping the annotations. We have designed a pipeline to obtain good-quality MSAs and to transfer annotations from any protein to their orthologs. Applying the pipeline to DisProt proteins, from the 1731 entries with 5623 annotations, we can reach 97,555 orthologs and transfer a total of 301,190 terms by homology. We also provide a web server for consulting the results of DisProt proteins and execute the pipeline for any other protein. The server Homology Transfer IDP (HoTIDP) is accessible at http://hotidp.leloir.org.ar. © 2023 The Authors. Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.},
note = {Cited by: 2; All Open Access, Hybrid Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Typhaine Paysan-Lafosse; Matthias Blum; Sara Chuguransky; Tiago Grego; Beatriz Lázaro Pinto; Gustavo A. Salazar; Maxwell L. Bileschi; Peer Bork; Alan Bridge; Lucy Colwell; Julian Gough; Daniel H. Haft; Ivica Letunić; Aron Marchler-Bauer; Huaiyu Mi; Darren A. Natale; Christine A. Orengo; Arun P. Pandurangan; Catherine Rivoire; Christian J. A. Sigrist; Ian Sillitoe; Narmada Thanki; Paul D. Thomas; Silvio C. E. Tosatto; Cathy H. Wu; Alex Bateman
InterPro in 2022 Journal Article
In: Nucleic Acids Research, vol. 51, no. D1, pp. D418 – D427, 2023, ISSN: 03051048, (Cited by: 934; All Open Access, Gold Open Access).
Abstract | Links:
@article{Paysan-Lafosse2023D418,
title = {InterPro in 2022},
author = {Typhaine Paysan-Lafosse and Matthias Blum and Sara Chuguransky and Tiago Grego and Beatriz L\'{a}zaro Pinto and Gustavo A. Salazar and Maxwell L. Bileschi and Peer Bork and Alan Bridge and Lucy Colwell and Julian Gough and Daniel H. Haft and Ivica Letuni\'{c} and Aron Marchler-Bauer and Huaiyu Mi and Darren A. Natale and Christine A. Orengo and Arun P. Pandurangan and Catherine Rivoire and Christian J. A. Sigrist and Ian Sillitoe and Narmada Thanki and Paul D. Thomas and Silvio C. E. Tosatto and Cathy H. Wu and Alex Bateman},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85159577204\&doi=10.109%2fna%2fgkac993\&partnerID=40\&md5=e46875f1af4e31a9a0b5bb0276e7a3a5},
doi = {10.1093/nar/gkac993},
issn = {03051048},
year = {2023},
date = {2023-01-01},
journal = {Nucleic Acids Research},
volume = {51},
number = {D1},
pages = {D418 \textendash D427},
publisher = {Oxford University Press},
abstract = {The InterPro database (https://www.ebi.ac.uk/ interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites. Here, we report recent developments with InterPro (version 90.0) and its associated software, including updates to data content and to the website. These developments extend and enrich the information provided by InterPro, and provide a more user friendly access to the data. Additionally, we have worked on adding Pfam website features to the InterPro website, as the Pfam website will be retired in late 2022. We also show that InterPro’s sequence coverage has kept pace with the growth of UniProtKB. Moreover, we report the development of a card game as a method of engaging the non-scientific community. Finally, we discuss the benefits and challenges brought by the use of artificial intelligence for protein structure prediction. © The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.},
note = {Cited by: 934; All Open Access, Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Books
Fotis Psomopoulos; Carole Coble; Leyla Jael Castro; Jennifer Harrow; Silvio C. E. Tosatto
A roadmap for defining machine learning standards in life sciences Book
World Scientific Publishing Co. Pte. Ltd., 2023, ISBN: 978-981126567-9; 978-981126566-2, (Cited by: 0).
@book{Psomopoulos2023399,
title = {A roadmap for defining machine learning standards in life sciences},
author = {Fotis Psomopoulos and Carole Coble and Leyla Jael Castro and Jennifer Harrow and Silvio C. E. Tosatto},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85161855618\&doi=10.114%2f9789811265679_0022\&partnerID=40\&md5=1386b69dc0acc0815feb44dfe8a4bf58},
doi = {10.1142/9789811265679_0022},
isbn = {978-981126567-9; 978-981126566-2},
year = {2023},
date = {2023-01-01},
journal = {Artificial Intelligence For Science: A Deep Learning Revolution},
pages = {399 \textendash 410},
publisher = {World Scientific Publishing Co. Pte. Ltd.},
note = {Cited by: 0},
keywords = {},
pubstate = {published},
tppubtype = {book}
}
2022
Journal Articles
Franco Pradelli; Giovanni Minervini; Silvio C. E. Tosatto
Mocafe: a comprehensive Python library for simulating cancer development with Phase Field Models Journal Article
In: Bioinformatics, vol. 38, no. 18, pp. 4440 – 4441, 2022, ISSN: 13674803, (Cited by: 1).
Abstract | Links:
@article{Pradelli20224440,
title = {Mocafe: a comprehensive Python library for simulating cancer development with Phase Field Models},
author = {Franco Pradelli and Giovanni Minervini and Silvio C. E. Tosatto},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85141891628\&doi=10.109%2fbioinformatic%2fbtac521\&partnerID=40\&md5=4d6f26134afd4ec6aa8b90a9c55bd40c},
doi = {10.1093/bioinformatics/btac521},
issn = {13674803},
year = {2022},
date = {2022-01-01},
journal = {Bioinformatics},
volume = {38},
number = {18},
pages = {4440 \textendash 4441},
publisher = {Oxford University Press},
abstract = {Summary: Mathematical models are effective in studying cancer development at different scales from metabolism to tissue. Phase Field Models (PFMs) have been shown to reproduce accurately cancer growth and other related phenomena, including expression of relevant molecules, extracellular matrix remodeling and angiogenesis. However, implementations of such models are rarely published, reducing access to these techniques. To reduce this gap, we developed Mocafe, a modular open-source Python package that implements some of the most important PFMs reported in the literature. Mocafe is designed to handle both PFMs purely based on differential equations and hybrid agent-based PFMs. Moreover, Mocafe is meant to be extensible, allowing the inclusion of new models in future releases. © 2022 The Author(s). Published by Oxford University Press. All rights reserved.},
note = {Cited by: 1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Damiano Piovesan; Alexander Miguel Monzon; Silvio C. E. Tosatto
Intrinsic protein disorder and conditional folding in AlphaFoldDB Journal Article
In: Protein Science, vol. 31, no. 11, 2022, ISSN: 09618368, (Cited by: 44; All Open Access, Hybrid Gold Open Access).
Abstract | Links:
@article{Piovesan2022,
title = {Intrinsic protein disorder and conditional folding in AlphaFoldDB},
author = {Damiano Piovesan and Alexander Miguel Monzon and Silvio C. E. Tosatto},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85141005149\&doi=10.100%2fpro.4466\&partnerID=40\&md5=8fac8ca44f3f4c34e62c585165baa7dc},
doi = {10.1002/pro.4466},
issn = {09618368},
year = {2022},
date = {2022-01-01},
journal = {Protein Science},
volume = {31},
number = {11},
publisher = {John Wiley and Sons Inc},
abstract = {Intrinsically disordered regions (IDRs) defying the traditional protein structure\textendashfunction paradigm have been difficult to analyze. The availability of accurate structure predictions on a large scale in AlphaFoldDB offers a fresh perspective on IDR prediction. Here, we establish three baselines for IDR prediction from AlphaFoldDB models based on the recent CAID dataset. Surprisingly, AlphaFoldDB is highly competitive for predicting both IDRs and conditionally folded binding regions, demonstrating the plasticity of the disorder to structure continuum. © 2022 The Authors. Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.},
note = {Cited by: 44; All Open Access, Hybrid Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Federica Quaglia; András Hatos; Edoardo Salladini; Damiano Piovesan; Silvio C. E. Tosatto
Exploring Manually Curated Annotations of Intrinsically Disordered Proteins with DisProt Journal Article
In: Current Protocols, vol. 2, no. 7, 2022, ISSN: 26911299, (Cited by: 4; All Open Access, Hybrid Gold Open Access).
Abstract | Links:
@article{Quaglia2022,
title = {Exploring Manually Curated Annotations of Intrinsically Disordered Proteins with DisProt},
author = {Federica Quaglia and Andr\'{a}s Hatos and Edoardo Salladini and Damiano Piovesan and Silvio C. E. Tosatto},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85133241328\&doi=10.100%2fcpz1.484\&partnerID=40\&md5=c0b162170006c7f2db3710e8b52eef9b},
doi = {10.1002/cpz1.484},
issn = {26911299},
year = {2022},
date = {2022-01-01},
journal = {Current Protocols},
volume = {2},
number = {7},
publisher = {John Wiley and Sons Inc},
abstract = {DisProt is the major repository of manually curated data for intrinsically disordered proteins collected from the literature. Although lacking a stable three-dimensional structure under physiological conditions, intrinsically disordered proteins carry out a plethora of biological functions, some of them directly arising from their flexible nature. A growing number of scientific studies have been published during the last few decades to shed light on their unstructured state, their binding modes, and their functions. DisProt makes use of a team of expert biocurators to provide up-to-date annotations of intrinsically disordered proteins from the literature, making them available to the scientific community. Here we present a comprehensive description on how to use DisProt in different contexts and provide a detailed explanation of how to explore and interpret manually curated annotations of intrinsically disordered proteins. We describe how to search DisProt annotations, both using the web interface and the API for programmatic access. Finally, we explain how to visualize and interpret a DisProt entry, the SARS-CoV-2 Nucleoprotein, characterized by the presence of unstructured N-terminal and C-terminal regions and a flexible linker. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Performing a search in DisProt. Support Protocol 1: Downloading options. Support Protocol 2: Programmatic access with DisProt REST API. Basic Protocol 2: Exploring the DisProt Ontology page. Basic Protocol 3: Visualizing and interpreting DisProt entries\textendashthe SARS-CoV-2 Nucleoprotein use case. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC.},
note = {Cited by: 4; All Open Access, Hybrid Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Margot A. Cousin; Emma L. Veale; Nikita R. Dsouza; Swarnendu Tripathi; Robyn G. Holden; Maria Arelin; Geoffrey Beek; Mir Reza Bekheirnia; Jasmin Beygo; Vikas Bhambhani; Martin Bialer; Stefania Bigoni; Cyrus Boelman; Jenny Carmichael; Thomas Courtin; Benjamin Cogne; Ivana Dabaj; Diane Doummar; Laura Fazilleau; Alessandra Ferlini; Ralitza H. Gavrilova; John M. Graham; Tobias B. Haack; Jane Juusola; Sarina G. Kant; Saima Kayani; Boris Keren; Petra Ketteler; Chiara Klöckner; Tamara T. Koopmann; Teresa M. Kruisselbrink; Alma Kuechler; Laëtitia Lambert; Xénia Latypova; Robert Roger Lebel; Magalie S. Leduc; Emanuela Leonardi; Andrea M. Lewis; Wendy Liew; Keren Machol; Samir Mardini; Kirsty McWalter; Cyril Mignot; Julie McLaughlin; Alessandra Murgia; Vinodh Narayanan; Caroline Nava; Sonja Neuser; Mathilde Nizon; Davide Ognibene; Joohyun Park; Konrad Platzer; Céline Poirsier; Maximilian Radtke; Keri Ramsey; Cassandra K. Runke; Maria J. Guillen Sacoto; Fernando Scaglia; Marwan Shinawi; Stephanie Spranger; Ee Shien Tan; John Taylor; Anne-Sophie Trentesaux; Filippo Vairo; Rebecca Willaert; Neda Zadeh; Raul Urrutia; Dusica Babovic-Vuksanovic; Michael T. Zimmermann; Alistair Mathie; Eric W. Klee
Gain and loss of TASK3 channel function and its regulation by novel variation cause KCNK9 imprinting syndrome Journal Article
In: Genome Medicine, vol. 14, no. 1, 2022, ISSN: 1756994X, (Cited by: 9; All Open Access, Gold Open Access, Green Open Access).
Abstract | Links:
@article{Cousin2022,
title = {Gain and loss of TASK3 channel function and its regulation by novel variation cause KCNK9 imprinting syndrome},
author = {Margot A. Cousin and Emma L. Veale and Nikita R. Dsouza and Swarnendu Tripathi and Robyn G. Holden and Maria Arelin and Geoffrey Beek and Mir Reza Bekheirnia and Jasmin Beygo and Vikas Bhambhani and Martin Bialer and Stefania Bigoni and Cyrus Boelman and Jenny Carmichael and Thomas Courtin and Benjamin Cogne and Ivana Dabaj and Diane Doummar and Laura Fazilleau and Alessandra Ferlini and Ralitza H. Gavrilova and John M. Graham and Tobias B. Haack and Jane Juusola and Sarina G. Kant and Saima Kayani and Boris Keren and Petra Ketteler and Chiara Kl\"{o}ckner and Tamara T. Koopmann and Teresa M. Kruisselbrink and Alma Kuechler and La\"{e}titia Lambert and X\'{e}nia Latypova and Robert Roger Lebel and Magalie S. Leduc and Emanuela Leonardi and Andrea M. Lewis and Wendy Liew and Keren Machol and Samir Mardini and Kirsty McWalter and Cyril Mignot and Julie McLaughlin and Alessandra Murgia and Vinodh Narayanan and Caroline Nava and Sonja Neuser and Mathilde Nizon and Davide Ognibene and Joohyun Park and Konrad Platzer and C\'{e}line Poirsier and Maximilian Radtke and Keri Ramsey and Cassandra K. Runke and Maria J. Guillen Sacoto and Fernando Scaglia and Marwan Shinawi and Stephanie Spranger and Ee Shien Tan and John Taylor and Anne-Sophie Trentesaux and Filippo Vairo and Rebecca Willaert and Neda Zadeh and Raul Urrutia and Dusica Babovic-Vuksanovic and Michael T. Zimmermann and Alistair Mathie and Eric W. Klee},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85131795908\&doi=10.118%2fs13073-022-01064-4\&partnerID=40\&md5=81531c1a0244ddf38e75235cde81e258},
doi = {10.1186/s13073-022-01064-4},
issn = {1756994X},
year = {2022},
date = {2022-01-01},
journal = {Genome Medicine},
volume = {14},
number = {1},
publisher = {BioMed Central Ltd},
abstract = {Background: Genomics enables individualized diagnosis and treatment, but large challenges remain to functionally interpret rare variants. To date, only one causative variant has been described for KCNK9 imprinting syndrome (KIS). The genotypic and phenotypic spectrum of KIS has yet to be described and the precise mechanism of disease fully understood. Methods: This study discovers mechanisms underlying KCNK9 imprinting syndrome (KIS) by describing 15 novel KCNK9 alterations from 47 KIS-affected individuals. We use clinical genetics and computer-assisted facial phenotyping to describe the phenotypic spectrum of KIS. We then interrogate the functional effects of the variants in the encoded TASK3 channel using sequence-based analysis, 3D molecular mechanic and dynamic protein modeling, and in vitro electrophysiological and functional methodologies. Results: We describe the broader genetic and phenotypic variability for KIS in a cohort of individuals identifying an additional mutational hotspot at p.Arg131 and demonstrating the common features of this neurodevelopmental disorder to include motor and speech delay, intellectual disability, early feeding difficulties, muscular hypotonia, behavioral abnormalities, and dysmorphic features. The computational protein modeling and in vitro electrophysiological studies discover variability of the impact of KCNK9 variants on TASK3 channel function identifying variants causing gain and others causing loss of conductance. The most consistent functional impact of KCNK9 genetic variants, however, was altered channel regulation. Conclusions: This study extends our understanding of KIS mechanisms demonstrating its complex etiology including gain and loss of channel function and consistent loss of channel regulation. These data are rapidly applicable to diagnostic strategies, as KIS is not identifiable from clinical features alone and thus should be molecularly diagnosed. Furthermore, our data suggests unique therapeutic strategies may be needed to address the specific functional consequences of KCNK9 variation on channel function and regulation. © 2022, The Author(s).},
note = {Cited by: 9; All Open Access, Gold Open Access, Green Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Mihaly Varadi; Stephen Anyango; David Armstrong; John Berrisford; Preeti Choudhary; Mandar Deshpande; Nurul Nadzirin; Sreenath S. Nair; Lukas Pravda; Ahsan Tanweer; Bissan Al-Lazikani; Claudia Andreini; Geoffrey J. Barton; David Bednar; Karel Berka; Tom Blundell; Kelly P. Brock; Jose Maria Carazo; Jiri Damborsky; Alessia David; Sucharita Dey; Roland Dunbrack; Juan Fernandez Recio; Franca Fraternali; Toby Gibson; Manuela Helmer-Citterich; David Hoksza; Thomas Hopf; David Jakubec; Natarajan Kannan; Radoslav Krivak; Manjeet Kumar; Emmanuel D. Levy; Nir London; Jose Ramon Macias; Madhusudhan M. Srivatsan; Debora S. Marks; Lennart Martens; Stuart A. McGowan; Jake E. McGreig; Vivek Modi; R. Gonzalo Parra; Gerardo Pepe; Damiano Piovesan; Jaime Prilusky; Valeria Putignano; Leandro G. Radusky; Pathmanaban Ramasamy; Atilio O. Rausch; Nathalie Reuter; Luis A. Rodriguez; Nathan J. Rollins; Antonio Rosato; Paweł Rubach; Luis Serrano; Gulzar Singh; Petr Skoda; Carlos Oscar S. Sorzano; Jan Stourac; Joanna I. Sulkowska; Radka Svobodova; Natalia Tichshenko; Silvio C. E. Tosatto; Wim Vranken; Mark N. Wass; Dandan Xue; Daniel Zaidman; Janet Thornton; Michael Sternberg; Christine Orengo; Sameer Velankar
PDBe-KB: collaboratively defining the biological context of structural data Journal Article
In: Nucleic Acids Research, vol. 50, no. D1, pp. D534 – D542, 2022, ISSN: 03051048, (Cited by: 49; All Open Access, Gold Open Access).
Abstract | Links:
@article{Varadi2022D534,
title = {PDBe-KB: collaboratively defining the biological context of structural data},
author = {Mihaly Varadi and Stephen Anyango and David Armstrong and John Berrisford and Preeti Choudhary and Mandar Deshpande and Nurul Nadzirin and Sreenath S. Nair and Lukas Pravda and Ahsan Tanweer and Bissan Al-Lazikani and Claudia Andreini and Geoffrey J. Barton and David Bednar and Karel Berka and Tom Blundell and Kelly P. Brock and Jose Maria Carazo and Jiri Damborsky and Alessia David and Sucharita Dey and Roland Dunbrack and Juan Fernandez Recio and Franca Fraternali and Toby Gibson and Manuela Helmer-Citterich and David Hoksza and Thomas Hopf and David Jakubec and Natarajan Kannan and Radoslav Krivak and Manjeet Kumar and Emmanuel D. Levy and Nir London and Jose Ramon Macias and Madhusudhan M. Srivatsan and Debora S. Marks and Lennart Martens and Stuart A. McGowan and Jake E. McGreig and Vivek Modi and R. Gonzalo Parra and Gerardo Pepe and Damiano Piovesan and Jaime Prilusky and Valeria Putignano and Leandro G. Radusky and Pathmanaban Ramasamy and Atilio O. Rausch and Nathalie Reuter and Luis A. Rodriguez and Nathan J. Rollins and Antonio Rosato and Pawe\l Rubach and Luis Serrano and Gulzar Singh and Petr Skoda and Carlos Oscar S. Sorzano and Jan Stourac and Joanna I. Sulkowska and Radka Svobodova and Natalia Tichshenko and Silvio C. E. Tosatto and Wim Vranken and Mark N. Wass and Dandan Xue and Daniel Zaidman and Janet Thornton and Michael Sternberg and Christine Orengo and Sameer Velankar},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85125170185\&doi=10.109%2fna%2fgkab988\&partnerID=40\&md5=9538f59308b4225433abd082b649630b},
doi = {10.1093/nar/gkab988},
issn = {03051048},
year = {2022},
date = {2022-01-01},
journal = {Nucleic Acids Research},
volume = {50},
number = {D1},
pages = {D534 \textendash D542},
publisher = {Oxford University Press},
abstract = {The Protein Data Bank in Europe \textendash Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Data Bank (PDB). The goal of PDBe-KB is to place macromolecular structure data in their biological context by developing standardised data exchange formats and integrating functional annotations from the contributing partner resources into a knowledge graph that can provide valuable biological insights. Since we described PDBe-KB in 2019, there have been significant improvements in the variety of available annotation data sets and user functionality. Here, we provide an overview of the consortium, highlighting the addition of annotations such as predicted covalent binders, phosphorylation sites, effects of mutations on the protein structure and energetic local frustration. In addition, we describe a library of reusable web-based visualisation components and introduce new features such as a bulk download data service and a novel superposition service that generates clusters of superposed protein chains weekly for the whole PDB archive. © The Author(s) 2021.},
note = {Cited by: 49; All Open Access, Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Alexander Miguel Monzon; Damiano Piovesan; Monika Fuxreiter
Molecular Determinants of Selectivity in Disordered Complexes May Shed Light on Specificity in Protein Condensates Journal Article
In: Biomolecules, vol. 12, no. 1, 2022, ISSN: 2218273X, (Cited by: 4; All Open Access, Gold Open Access, Green Open Access).
Abstract | Links:
@article{Monzon2022,
title = {Molecular Determinants of Selectivity in Disordered Complexes May Shed Light on Specificity in Protein Condensates},
author = {Alexander Miguel Monzon and Damiano Piovesan and Monika Fuxreiter},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85122180762\&doi=10.339%2fbiom12010092\&partnerID=40\&md5=68363b8c137547c19a70094b1da39526},
doi = {10.3390/biom12010092},
issn = {2218273X},
year = {2022},
date = {2022-01-01},
journal = {Biomolecules},
volume = {12},
number = {1},
publisher = {MDPI},
abstract = {Biomolecular condensates challenge the classical concepts of molecular recognition. The variable composition and heterogeneous conformations of liquid‐like protein droplets are bottlenecks for high‐resolution structural studies. To obtain atomistic insights into the organization of these assemblies, here we have characterized the conformational ensembles of specific disordered complexes, including those of droplet‐driving proteins. First, we found that these specific complexes exhibit a high degree of conformational heterogeneity. Second, we found that residues forming contacts at the interface also sample many conformations. Third, we found that different patterns of contacting residues form the specific interface. In addition, we observed a wide range of sequence motifs mediating disordered interactions, including charged, hydrophobic and polar contacts. These results demonstrate that selective recognition can be realized by variable patterns of weakly defined interaction motifs in many different binding configurations. We propose that these principles also play roles in determining the selectivity of biomolecular condensates. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.},
note = {Cited by: 4; All Open Access, Gold Open Access, Green Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Antonella Falconieri; Giovanni Minervini; Federica Quaglia; Geppo Sartori; Silvio C. E. Tosatto
Characterization of the pVHL Interactome in Human Testis Using High-Throughput Library Screening Journal Article
In: Cancers, vol. 14, no. 4, 2022, ISSN: 20726694, (Cited by: 1; All Open Access, Gold Open Access).
Abstract | Links:
@article{Falconieri2022,
title = {Characterization of the pVHL Interactome in Human Testis Using High-Throughput Library Screening},
author = {Antonella Falconieri and Giovanni Minervini and Federica Quaglia and Geppo Sartori and Silvio C. E. Tosatto},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85124955220\&doi=10.339%2fcancers14041009\&partnerID=40\&md5=a1ec0d6bae3dd398c489f828c58a9d04},
doi = {10.3390/cancers14041009},
issn = {20726694},
year = {2022},
date = {2022-01-01},
journal = {Cancers},
volume = {14},
number = {4},
publisher = {MDPI},
abstract = {Functional impairment of the von Hippel\textendashLindau tumor suppressor (pVHL) is causative of a familiar increased risk of developing cancer. As an E3 substrate recognition particle, pVHL marks the hypoxia inducible factor 1α (HIF-1α) for degradation in normoxic conditions, thus acting as a key regulator of both acute and chronic cell adaptation to hypoxia. The male mice model carrying VHL gene conditional knockout presents significant abnormalities in testis development paired with defects in spermatogenesis and infertility, indicating that pVHL exerts testis-specific roles. Here we aimed to explore whether pVHL could have a similar role in humans by performing a testis-tissue library screening complemented with in-depth bioinformatics analysis. We identified 55 novel pVHL binding proteins directly involved in spermatogenesis, cell differentiation and reproductive metabolism. In addition, computational investigation of these new interactors identified multiple pVHL-specific binding motifs and demonstrated that somatic mutations described in human cancers reside in these binding regions. Collectively, these findings suggest that, in addition to its role in cancer formation, pVHL may also be pivotal in normal gonadal development in humans. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.},
note = {Cited by: 1; All Open Access, Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Andras Hatos; Alexander Miguel Monzon; Silvio C. E. Tosatto; Damiano Piovesan; Monika Fuxreiter
FuzDB: A new phase in understanding fuzzy interactions Journal Article
In: Nucleic Acids Research, vol. 50, no. D1, pp. D509 – D517, 2022, ISSN: 03051048, (Cited by: 31; All Open Access, Gold Open Access, Green Open Access).
Abstract | Links:
@article{Hatos2022D509,
title = {FuzDB: A new phase in understanding fuzzy interactions},
author = {Andras Hatos and Alexander Miguel Monzon and Silvio C. E. Tosatto and Damiano Piovesan and Monika Fuxreiter},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85122220907\&doi=10.109%2fna%2fgkab1060\&partnerID=40\&md5=4987bea33a75620f0883d6e23e5a026e},
doi = {10.1093/nar/gkab1060},
issn = {03051048},
year = {2022},
date = {2022-01-01},
journal = {Nucleic Acids Research},
volume = {50},
number = {D1},
pages = {D509 \textendash D517},
publisher = {Oxford University Press},
abstract = {Fuzzy interactions are specific, variable contacts between proteins and other biomolecules (proteins, DNA, RNA, small molecules) formed in accord to the cellular context. Fuzzy interactions have recently been demonstrated to regulate biomolecular condensates generated by liquid-liquid phase separation. The FuzDB v4.0 database (https://fuzdb.org) assembles experimentally identified examples of fuzzy interactions, where disordered regions mediate functionally important, context-dependent contacts between the partners in stoichiometric and higher-order assemblies. The new version of FuzDB establishes cross-links with databases on structure (PDB, BMRB, PED), function (ELM, UniProt) and biomolecular condensates (PhaSepDB, PhaSePro, LLPSDB). FuzDB v4.0 is a source to decipher molecular basis of complex cellular interaction behaviors, including those in protein droplets. © 2022 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.},
note = {Cited by: 31; All Open Access, Gold Open Access, Green Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Emanuela Leonardi; Castrense Savojardo; Giovanni Minervini
Molecular Effects of Mutations in Human Genetic Diseases Journal Article
In: International Journal of Molecular Sciences, vol. 23, no. 12, 2022, ISSN: 16616596, (Cited by: 0; All Open Access, Gold Open Access).
@article{Leonardi2022,
title = {Molecular Effects of Mutations in Human Genetic Diseases},
author = {Emanuela Leonardi and Castrense Savojardo and Giovanni Minervini},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85131521999\&doi=10.339%2fijms23126408\&partnerID=40\&md5=c6680514435110fbec490e986071e267},
doi = {10.3390/ijms23126408},
issn = {16616596},
year = {2022},
date = {2022-01-01},
journal = {International Journal of Molecular Sciences},
volume = {23},
number = {12},
publisher = {MDPI},
note = {Cited by: 0; All Open Access, Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Federica Quaglia; Bálint Meszáros; Edoardo Salladini; András Hatos; Rita Pancsa; Lucía B. Chemes; Mátyás Pajkos; Tamas Lazar; Samuel Peña-Díaz; Jaime Santos; Veronika Ács; Nazanin Farahi; Erzsebet Fichó; Maria Cristina Aspromonte; Claudio Bassot; Anastasia Chasapi; Norman E. Davey; Radoslav Davidović; Laszlo Dobson; Arne Elofsson; Gábor Erdos; Pascale Gaudet; Michelle Giglio; Juliana Glavina; Javier Iserte; Valentín Iglesias; Zsófia Kálmán; Matteo Lambrughi; Emanuela Leonardi; Sonia Longhi; Sandra Macedo-Ribeiro; Emiliano Maiani; Julia Marchetti; Cristina Marino-Buslje; Attila Meszáros; Alexander Miguel Monzon; Giovanni Minervini; Suvarna Nadendla; Juliet F. Nilsson; Marian Novotný; Christos A. Ouzounis; Nicolás Palopoli; Elena Papaleo; Pedro Jose Barbosa Pereira; Gabriele Pozzati; Vasilis J. Promponas; Jordi Pujols; Alma Carolina Sanchez Rocha; Martin Salas; Luciana Rodriguez Sawicki; Eva Schad; Aditi Shenoy; Tamás Szaniszló; Konstantinos D. Tsirigos; Nevena Veljkovic; Gustavo Parisi; Salvador Ventura; Zsuzsanna Dosztányi; Peter Tompa; Silvio C. E. Tosatto; Damiano Piovesan
DisProt in 2022: Improved quality and accessibility of protein intrinsic disorder annotation Journal Article
In: Nucleic Acids Research, vol. 50, no. D1, pp. D480 – D487, 2022, ISSN: 03051048, (Cited by: 110; All Open Access, Gold Open Access).
Abstract | Links:
@article{Quaglia2022D480,
title = {DisProt in 2022: Improved quality and accessibility of protein intrinsic disorder annotation},
author = {Federica Quaglia and B\'{a}lint Mesz\'{a}ros and Edoardo Salladini and Andr\'{a}s Hatos and Rita Pancsa and Luc\'{i}a B. Chemes and M\'{a}ty\'{a}s Pajkos and Tamas Lazar and Samuel Pe\~{n}a-D\'{i}az and Jaime Santos and Veronika \'{A}cs and Nazanin Farahi and Erzsebet Fich\'{o} and Maria Cristina Aspromonte and Claudio Bassot and Anastasia Chasapi and Norman E. Davey and Radoslav Davidovi\'{c} and Laszlo Dobson and Arne Elofsson and G\'{a}bor Erdos and Pascale Gaudet and Michelle Giglio and Juliana Glavina and Javier Iserte and Valent\'{i}n Iglesias and Zs\'{o}fia K\'{a}lm\'{a}n and Matteo Lambrughi and Emanuela Leonardi and Sonia Longhi and Sandra Macedo-Ribeiro and Emiliano Maiani and Julia Marchetti and Cristina Marino-Buslje and Attila Mesz\'{a}ros and Alexander Miguel Monzon and Giovanni Minervini and Suvarna Nadendla and Juliet F. Nilsson and Marian Novotn\'{y} and Christos A. Ouzounis and Nicol\'{a}s Palopoli and Elena Papaleo and Pedro Jose Barbosa Pereira and Gabriele Pozzati and Vasilis J. Promponas and Jordi Pujols and Alma Carolina Sanchez Rocha and Martin Salas and Luciana Rodriguez Sawicki and Eva Schad and Aditi Shenoy and Tam\'{a}s Szaniszl\'{o} and Konstantinos D. Tsirigos and Nevena Veljkovic and Gustavo Parisi and Salvador Ventura and Zsuzsanna Doszt\'{a}nyi and Peter Tompa and Silvio C. E. Tosatto and Damiano Piovesan},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85125157608\&doi=10.109%2fna%2fgkab1082\&partnerID=40\&md5=270bf5618598238b9e614e8070e3723a},
doi = {10.1093/nar/gkab1082},
issn = {03051048},
year = {2022},
date = {2022-01-01},
journal = {Nucleic Acids Research},
volume = {50},
number = {D1},
pages = {D480 \textendash D487},
publisher = {Oxford University Press},
abstract = {The Database of Intrinsically Disordered Proteins (DisProt, URL: https://disprot.org) is the major repository of manually curated annotations of intrinsically disordered proteins and regions from the literature. We report here recent updates of DisProt version 9, including a restyled web interface, refactored Intrinsically Disordered Proteins Ontology (IDPO), improvements in the curation process and significant content growth of around 3%. Higher quality and consistency of annotations is provided by a newly implemented reviewing process and training of curators. The increased curation capacity is fostered by the integration of DisProt with APICURON, a dedicated resource for the proper attribution and recognition of biocuration efforts. Better interoperability is provided through the adoption of the Minimum Information About Disorder (MIADE) standard, an active collaboration with the Gene Ontology (GO) and Evidence and Conclusion Ontology (ECO) consortia and the support of the ELIXIR infrastructure. © 2022 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.},
note = {Cited by: 110; All Open Access, Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Martina Bevilacqua; Lisanna Paladin; Silvio C. E. Tosatto; Damiano Piovesan
ProSeqViewer: an interactive, responsive and efficient TypeScript library for visualization of sequences and alignments in web applications Journal Article
In: Bioinformatics, vol. 38, no. 4, pp. 1129 – 1130, 2022, ISSN: 13674803, (Cited by: 5).
Abstract | Links:
@article{Bevilacqua20221129,
title = {ProSeqViewer: an interactive, responsive and efficient TypeScript library for visualization of sequences and alignments in web applications},
author = {Martina Bevilacqua and Lisanna Paladin and Silvio C. E. Tosatto and Damiano Piovesan},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85130453196\&doi=10.109%2fbioinformatic%2fbtab764\&partnerID=40\&md5=c8c0d4a29d86a08880a568a5b8eac3bb},
doi = {10.1093/bioinformatics/btab764},
issn = {13674803},
year = {2022},
date = {2022-01-01},
journal = {Bioinformatics},
volume = {38},
number = {4},
pages = {1129 \textendash 1130},
publisher = {Oxford University Press},
abstract = {Biological data is ever-increasing in amount and complexity. The mapping of this data to biological entities such as nucleotide and amino acid sequences supports biological data analysis, classification and prediction. Sequence alignments and comparison allow the transfer of knowledge to evolutionary-related entities, the mapping of functional domains, the identification of binding and modification sites. To support these types of studies, we developed ProSeqViewer, a tool to visualize annotation on single sequences and multiple sequence alignments. This state-of-the-art multifunctional library was developed as a modular component to be integrated into static or dynamic web resources and support intuitive visualization of sequence features. ProseSeqViewer is extremely lightweight, fast, interactive, dynamic, responsive and works at any screen size. It generates pure HTML which is compatible with any browser and operating system. ProSeqViewer can exchange events with other visualization components and is already used by multiple biological databases. © 2022 Oxford University Press. All rights reserved.},
note = {Cited by: 5},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Damiano Piovesan; Miguel Arbesú; Monika Fuxreiter; Miquel Pons
Editorial: Fuzzy Interactions: Many Facets of Protein Binding Journal Article
In: Frontiers in Molecular Biosciences, vol. 9, 2022, ISSN: 2296889X, (Cited by: 3; All Open Access, Gold Open Access, Green Open Access).
@article{Piovesan2022b,
title = {Editorial: Fuzzy Interactions: Many Facets of Protein Binding},
author = {Damiano Piovesan and Miguel Arbes\'{u} and Monika Fuxreiter and Miquel Pons},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85133657451\&doi=10.338%2ffmolb.2022.947215\&partnerID=40\&md5=59607f7f0de31dcedef11e74b846f4bd},
doi = {10.3389/fmolb.2022.947215},
issn = {2296889X},
year = {2022},
date = {2022-01-01},
journal = {Frontiers in Molecular Biosciences},
volume = {9},
publisher = {Frontiers Media S.A.},
note = {Cited by: 3; All Open Access, Gold Open Access, Green Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Damiano Clementel; Alessio Del Conte; Alexander Miguel Monzon; Giorgia F Camagni; Giovanni Minervini; Damiano Piovesan; Silvio C. E Tosatto
RING 3.0: fast generation of probabilistic residue interaction networks from structural ensembles Journal Article
In: Nucleic Acids Research, vol. 50, no. W1, pp. W651 – W656, 2022, ISSN: 03051048, (Cited by: 86; All Open Access, Gold Open Access, Green Open Access).
Abstract | Links:
@article{Clementel2022W651,
title = {RING 3.0: fast generation of probabilistic residue interaction networks from structural ensembles},
author = {Damiano Clementel and Alessio Del Conte and Alexander Miguel Monzon and Giorgia F Camagni and Giovanni Minervini and Damiano Piovesan and Silvio C. E Tosatto},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85134391344\&doi=10.109%2fna%2fgkac365\&partnerID=40\&md5=b97a49e2ca7e88f01ad20ecc84f3780a},
doi = {10.1093/nar/gkac365},
issn = {03051048},
year = {2022},
date = {2022-01-01},
journal = {Nucleic Acids Research},
volume = {50},
number = {W1},
pages = {W651 \textendash W656},
publisher = {Oxford University Press},
abstract = {Residue interaction networks (RINs) are used to represent residue contacts in protein structures. Thanks to the advances in network theory, RINs have been proved effective as an alternative to coordinate data in the analysis of complex systems. The RING server calculates high quality and reliable non-covalent molecular interactions based on geometrical parameters. Here, we present the new RING 3.0 version extending the previous functionality in several ways. The underlying software library has been re-engineered to improve speed by an order of magnitude. RING now also supports the mmCIF format and provides typed interactions for the entire PDB chemical component dictionary, including nucleic acids. Moreover, RING now employs probabilistic graphs, where multiple conformations (e.g. NMR or molecular dynamics ensembles) are mapped as weighted edges, opening up new ways to analyze structural data. The web interface has been expanded to include a simultaneous view of the RIN alongside a structure viewer, with both synchronized and clickable. Contact evolution across models (or time) is displayed as a heatmap and can help in the discovery of correlating interaction patterns. The web server, together with an extensive help and tutorial, is available from URL: https://ring.biocomputingup.it/. © 2022 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.},
note = {Cited by: 86; All Open Access, Gold Open Access, Green Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Federica Quaglia; Edoardo Salladini; Marco Carraro; Giovanni Minervini; Silvio C. E. Tosatto; Philippe Le Mercier
SARS-CoV-2 variants preferentially emerge at intrinsically disordered protein sites helping immune evasion Journal Article
In: FEBS Journal, vol. 289, no. 14, pp. 4240 – 4250, 2022, ISSN: 1742464X, (Cited by: 22; All Open Access, Hybrid Gold Open Access).
Abstract | Links:
@article{Quaglia20224240,
title = {SARS-CoV-2 variants preferentially emerge at intrinsically disordered protein sites helping immune evasion},
author = {Federica Quaglia and Edoardo Salladini and Marco Carraro and Giovanni Minervini and Silvio C. E. Tosatto and Philippe Le Mercier},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85124603120\&doi=10.111%2ffebs.16379\&partnerID=40\&md5=2fe62fb69ba15243802da875a85f697d},
doi = {10.1111/febs.16379},
issn = {1742464X},
year = {2022},
date = {2022-01-01},
journal = {FEBS Journal},
volume = {289},
number = {14},
pages = {4240 \textendash 4250},
publisher = {John Wiley and Sons Inc},
abstract = {The SARS-CoV-2 pandemic is maintained by the emergence of successive variants, highlighting the flexibility of the protein sequences of the virus. We show that experimentally determined intrinsically disordered regions (IDRs) are abundant in the SARS-CoV-2 viral proteins, making up to 2% of disorder content for the S1 subunit of spike and up to 5% for the nucleoprotein, with the vast majority of mutations occurring in the 13 major variants mapped to these IDRs. Strikingly, antigenic sites are enriched in IDRs, in the receptor-binding domain (RBD) and in the N-terminal domain (NTD), suggesting a key role of structural flexibility in the antigenicity of the SARS-CoV-2 protein surface. Mutations occurring in the S1 subunit and nucleoprotein (N) IDRs are critical for immune evasion and antibody escape, suggesting potential additional implications for vaccines and monoclonal therapeutic strategies. Overall, this suggests the presence of variable regions on S1 and N protein surfaces, which confer sequence and antigenic flexibility to the virus without altering its protein functions. © 2022 The Authors. The FEBS Journal published by John Wiley \& Sons Ltd on behalf of Federation of European Biochemical Societies.},
note = {Cited by: 22; All Open Access, Hybrid Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Andras Hatos; Silvio C. E Tosatto; Michele Vendruscolo; Monika Fuxreiter
FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid-liquid phase separation and aggregation of proteins Journal Article
In: Nucleic Acids Research, vol. 50, no. W1, pp. W337 – W344, 2022, ISSN: 03051048, (Cited by: 55; All Open Access, Gold Open Access).
Abstract | Links:
@article{Hatos2022W337,
title = {FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid-liquid phase separation and aggregation of proteins},
author = {Andras Hatos and Silvio C. E Tosatto and Michele Vendruscolo and Monika Fuxreiter},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85134406800\&doi=10.109%2fna%2fgkac386\&partnerID=40\&md5=293978de7e452d8cb9f59ca16ea93afb},
doi = {10.1093/nar/gkac386},
issn = {03051048},
year = {2022},
date = {2022-01-01},
journal = {Nucleic Acids Research},
volume = {50},
number = {W1},
pages = {W337 \textendash W344},
publisher = {Oxford University Press},
abstract = {Many proteins perform their functions within membraneless organelles, where they form a liquid-like condensed state, also known as droplet state. The FuzDrop method predicts the probability of spontaneous liquid-liquid phase separation of proteins and provides a sequence-based score to identify the regions that promote this process. Furthermore, the FuzDrop method estimates the propensity of conversion of proteins to the amyloid state, and identifies aggregation hot-spots, which can drive the irreversible maturation of the liquid-like droplet state. These predictions can also identify mutations that can induce formation of amyloid aggregates, including those implicated in human diseases. To facilitate the interpretation of the predictions, the droplet-promoting and aggregation-promoting regions can be visualized on protein structures generated by AlphaFold. The FuzDrop server (https://fuzdrop.bio.unipd.it) thus offers insights into the complex behavior of proteins in their condensed states and facilitates the understanding of the functional relationships of proteins. © 2022 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.},
note = {Cited by: 55; All Open Access, Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
David E. Godler; Ling Ling; Dinusha Gamage; Emma K. Baker; Minh Bui; Michael J. Field; Carolyn Rogers; Merlin G. Butler; Alessandra Murgia; Emanuela Leonardi; Roberta Polli; Charles E. Schwartz; Cindy D. Skinner; Angelica M. Alliende; Lorena Santa Maria; James Pitt; Ronda Greaves; David Francis; Ralph Oertel; Min Wang; Cas Simons; David J. Amor
Feasibility of Screening for Chromosome 15 Imprinting Disorders in 16579 Newborns by Using a Novel Genomic Workflow Journal Article
In: JAMA Network Open, vol. 5, no. 1, 2022, ISSN: 25743805, (Cited by: 17; All Open Access, Gold Open Access, Green Open Access).
Abstract | Links:
@article{Godler2022,
title = {Feasibility of Screening for Chromosome 15 Imprinting Disorders in 16579 Newborns by Using a Novel Genomic Workflow},
author = {David E. Godler and Ling Ling and Dinusha Gamage and Emma K. Baker and Minh Bui and Michael J. Field and Carolyn Rogers and Merlin G. Butler and Alessandra Murgia and Emanuela Leonardi and Roberta Polli and Charles E. Schwartz and Cindy D. Skinner and Angelica M. Alliende and Lorena Santa Maria and James Pitt and Ronda Greaves and David Francis and Ralph Oertel and Min Wang and Cas Simons and David J. Amor},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85122738953\&doi=10.100%2fjamanetworkopen.2021.41911\&partnerID=40\&md5=32c9ffb6cf9d94db2d9f3bd72f534d93},
doi = {10.1001/jamanetworkopen.2021.41911},
issn = {25743805},
year = {2022},
date = {2022-01-01},
journal = {JAMA Network Open},
volume = {5},
number = {1},
publisher = {American Medical Association},
abstract = {Importance: Newborn screening for Angelman syndrome (AS), Prader-Willi syndrome (PWS), and chromosome 15 duplication syndrome (Dup15q) may lead to benefit from early diagnosis and treatment. Objective: To examine the feasibility of newborn screening for these chromosome 15 imprinting disorders at population scale. Design, Setting, and Participants: In this diagnostic study, the validation data set for the first-tier SNRPN test, called methylation-specific quantitative melt analysis (MS-QMA), included 109 PWS, 48 AS, 9 Dup15q, and 1190 population control newborn blood spots (NBS) and peripheral tissue samples from participants recruited from January 2000 to December 2016. The test data set included NBS samples from 16579 infants born in 2011. Infants with an NBS identified as positive for PWS, AS, or Dup15q by the first-tier test were referred for droplet digital polymerase chain reaction, real-time polymerase chain reaction, and low-coverage whole-genome sequencing for confirmatory testing. Data analyses were conducted between February 12, 2015, and August 15, 2020. Results: In the validation data set, the median age for the 77 patients with PWS was 3.00 years (IQR, 0.01-44.50 years); for the 46 patients with AS, 2.76 years (IQR, 0.028 to 49.00 years); and for the 9 patients with Dup15q, 4.00 years (IQR, 1.00 to 28.00 years). Thirty-eight patients (51.%) in the PWS group, 20 patients (45.%) in the AS group, and 6 patients (66.%) in the Dup15q group who had sex reported were male. The validation data set showed MS-QMA sensitivity of 99.% for PWS, 93.% for AS, and 77.% for Dup15q; specificity of 10% for PWS, AS, and Dup15q; positive predictive and negative predictive values of 10% for PWS and AS; and a positive predictive value of 87.% and negative predictive value of 10% for Dup15q. In the test data set of NBS samples from 16579 infants, 92 had a positive test result using a methylation ratio cut-off of 3 standard deviations from the mean. Of these patients, 2 were confirmed to have PWS; 2, AS; and 1, maternal Dup15q. With the use of more conservative PWS- and AS-specific thresholds for positive calls from the validation data set, 9 positive NBS results were identified by MS-QMA in this cohort. The 2 PWS and 2 AS calls were confirmed by second-tier testing, but the 1 Dup15q case was not confirmed. Together, these results provided prevalence estimates of 1 in 8290 for both AS and PWS and 1 in 16579 for maternal Dup15q, with positive predictive values for first-tier testing at 67.% for AS, 33.% for PWS, and 44.% for combined detection of chromosome 15 imprinting disorders for the validation data set. Conclusions and Relevance: The findings of this diagnostic study suggest that it is feasible to screen for all chromosome 15 imprinting disorders using SNRPN methylation analysis, with 5 individuals identified with these disorders out of 16579 infants screened.. © 2022 American Medical Association. All rights reserved.},
note = {Cited by: 17; All Open Access, Gold Open Access, Green Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Suvarna Nadendla; Rebecca Jackson; James Munro; Federica Quaglia; Bálint Mészáros; Dustin Olley; Elizabeth T. Hobbs; Stephen M. Goralski; Marcus Chibucos; Christopher John Mungall; Silvio C. E. Tosatto; Ivan Erill; Michelle G. Giglio
ECO: The Evidence and Conclusion Ontology, an update for 2022 Journal Article
In: Nucleic Acids Research, vol. 50, no. D1, pp. D1515 – D1521, 2022, ISSN: 03051048, (Cited by: 23; All Open Access, Gold Open Access).
Abstract | Links:
@article{Nadendla2022D1515,
title = {ECO: The Evidence and Conclusion Ontology, an update for 2022},
author = {Suvarna Nadendla and Rebecca Jackson and James Munro and Federica Quaglia and B\'{a}lint M\'{e}sz\'{a}ros and Dustin Olley and Elizabeth T. Hobbs and Stephen M. Goralski and Marcus Chibucos and Christopher John Mungall and Silvio C. E. Tosatto and Ivan Erill and Michelle G. Giglio},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85123230658\&doi=10.109%2fna%2fgkab1025\&partnerID=40\&md5=1c0f0bace596f47b96e7fc69267329dc},
doi = {10.1093/nar/gkab1025},
issn = {03051048},
year = {2022},
date = {2022-01-01},
journal = {Nucleic Acids Research},
volume = {50},
number = {D1},
pages = {D1515 \textendash D1521},
publisher = {Oxford University Press},
abstract = {The Evidence and Conclusion Ontology (ECO) is a community resource that provides an ontology of terms used to capture the type of evidence that supports biomedical annotations and assertions. Consistent capture of evidence information with ECO allows tracking of annotation provenance, establishment of quality control measures, and evidence-based data mining. ECO is in use by dozens of data repositories and resources with both specific and general areas of focus. ECO is continually being expanded and enhanced in response to user requests as well as our aim to adhere to community best-practices for ontology development. The ECO support team engages in multiple collaborations with other ontologies and annotating groups. Here we report on recent updates to the ECO ontology itself as well as associated resources that are available through this project. © 2022 The Author(s).},
note = {Cited by: 23; All Open Access, Gold Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Nahuel Escobedo; Ronaldo Romario Tunque Cahui; Gastón Caruso; Emilio García Ríos; Layla Hirsh; Alexander Miguel Monzon; Gustavo Parisi; Nicolas Palopoli
CoDNaS-Q: a database of conformational diversity of the native state of proteins with quaternary structure Journal Article
In: Bioinformatics, vol. 38, no. 21, pp. 4959 – 4961, 2022, ISSN: 13674803, (Cited by: 1; All Open Access, Bronze Open Access).
Abstract | Links:
@article{Escobedo20224959,
title = {CoDNaS-Q: a database of conformational diversity of the native state of proteins with quaternary structure},
author = {Nahuel Escobedo and Ronaldo Romario Tunque Cahui and Gast\'{o}n Caruso and Emilio Garc\'{i}a R\'{i}os and Layla Hirsh and Alexander Miguel Monzon and Gustavo Parisi and Nicolas Palopoli},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85141004727\&doi=10.109%2fbioinformatic%2fbtac627\&partnerID=40\&md5=ee4d714dba468725c6c3ccc7dbf78bb4},
doi = {10.1093/bioinformatics/btac627},
issn = {13674803},
year = {2022},
date = {2022-01-01},
journal = {Bioinformatics},
volume = {38},
number = {21},
pages = {4959 \textendash 4961},
publisher = {Oxford University Press},
abstract = {A collection of conformers that exist in a dynamical equilibrium defines the native state of a protein. The structural differences between them describe their conformational diversity, a defining characteristic of the protein with an essential role in multiple cellular processes. Since most proteins carry out their functions by assembling into complexes, we have developed CoDNaS-Q, the first online resource to explore conformational diversity in homooligomeric proteins. It features a curated collection of redundant protein structures with known quaternary structure. CoDNaS-Q integrates relevant annotations that allow researchers to identify and explore the extent and possible reasons of conformational diversity in homooligomeric protein complexes. © The Author(s) 2022. Published by Oxford University Press. All rights reserved.},
note = {Cited by: 1; All Open Access, Bronze Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}