PUBLICATIONS

@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=10.1093%2fdatabase%2fbaae009\&partnerID=40\&md5=df4fca19479789139b3fd19bb35c817f},

doi = {10.1093/database/baae009},

issn = {17580463},

year  = {2024},

date = {2024-01-01},

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}

}

@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=10.1002%2fbiof.2086\&partnerID=40\&md5=aff1210a238a2481081bf8c704ba8ef5},

doi = {10.1002/biof.2086},

issn = {09516433},

year  = {2024},

date = {2024-01-01},

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}

}

@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=10.1093%2fnar%2fgkae337\&partnerID=40\&md5=bca70d16fbb39f5466a3957673ef9eef},

doi = {10.1093/nar/gkae337},

issn = {03051048},

year  = {2024},

date = {2024-01-01},

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}

}

@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=10.1093%2fbioadv%2fvbae043\&partnerID=40\&md5=b6e09ea188a60708097f5bc31ba115dd},

doi = {10.1093/bioadv/vbae043},

issn = {26350041},

year  = {2024},

date = {2024-01-01},

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}

}

@article{Jain2024,

title = {CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods},

author = { },

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85187866396\&doi=10.1186%2fs13059-023-03113-6\&partnerID=40\&md5=9018a0ff0bf322ce7b902a3f07d71876},

doi = {10.1186/s13059-023-03113-6},

issn = {14747596},

year  = {2024},

date = {2024-01-01},

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: 10; All Open Access, Gold Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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=10.3390%2fgenes15091167\&partnerID=40\&md5=4358b236c257d898f6c44e2639ebbd9d},

doi = {10.3390/genes15091167},

issn = {20734425},

year  = {2024},

date = {2024-01-01},

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}

}

@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=10.1002%2fpro.4914\&partnerID=40\&md5=9d3ca7169c5c85e7e43289adbe2c3e24},

doi = {10.1002/pro.4914},

issn = {09618368},

year  = {2024},

date = {2024-01-01},

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}

}

@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=10.3390%2fijms25052994\&partnerID=40\&md5=36bf2bfc0d625c28b50aab098d0d94e7},

doi = {10.3390/ijms25052994},

issn = {16616596},

year  = {2024},

date = {2024-01-01},

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},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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=10.1093%2fnar%2fgkad947\&partnerID=40\&md5=0ad51562357f3e5f603d744e02f8729a},

doi = {10.1093/nar/gkad947},

issn = {03051048},

year  = {2024},

date = {2024-01-01},

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: 10; All Open Access, Gold Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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=10.1093%2fnar%2fgkad928\&partnerID=40\&md5=fc34ce08667ff42029fdb54d5142c08f},

doi = {10.1093/nar/gkad928},

issn = {03051048},

year  = {2024},

date = {2024-01-01},

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: 10; All Open Access, Gold Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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=10.1016%2fj.jsb.2023.108001\&partnerID=40\&md5=a32d9f45912f167f7d63dd4ecf4c4758},

doi = {10.1016/j.jsb.2023.108001},

issn = {10478477},

year  = {2023},

date = {2023-01-01},

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}

}

@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=10.1210%2fclinem%2fdgac671\&partnerID=40\&md5=b7a9f7deadbf767f38e0f33108febd94},

doi = {10.1210/clinem/dgac671},

issn = {0021972X},

year  = {2023},

date = {2023-01-01},

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 (1.6%) 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, 95% 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 3.4% in oligozoospermic subjects with T ≥ 15.38 nmol/L. Conversely, more than 80% 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}

}

@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=10.1002%2fcpz1.764\&partnerID=40\&md5=01fcae4cfec9f15a0d39dfdc6d05c8ab},

doi = {10.1002/cpz1.764},

issn = {26911299},

year  = {2023},

date = {2023-01-01},

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}

}

@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=10.1002%2fprot.26582\&partnerID=40\&md5=20d7d0ec6f796c0901f2a365becf7fa6},

doi = {10.1002/prot.26582},

issn = {08873585},

year  = {2023},

date = {2023-01-01},

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: 19; All Open Access, Hybrid Gold Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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=10.1093%2fnar%2fgkac1065\&partnerID=40\&md5=8547b341a7698891915b9e425ab793e7},

doi = {10.1093/nar/gkac1065},

issn = {03051048},

year  = {2023},

date = {2023-01-01},

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: 57; All Open Access, Gold Open Access, Green Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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=10.1126%2fsciadv.ade1694\&partnerID=40\&md5=47b819a09fd41c1bb6bde30c1401e4f7},

doi = {10.1126/sciadv.ade1694},

issn = {23752548},

year  = {2023},

date = {2023-01-01},

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}

}

@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=10.3390%2fijms24054710\&partnerID=40\&md5=90d98f8ae45a38cd27ab4323af8ae2b6},

doi = {10.3390/ijms24054710},

issn = {16616596},

year  = {2023},

date = {2023-01-01},

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}

}

@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=10.1093%2fnar%2fgkad430\&partnerID=40\&md5=a458ba56037429c6a042f7610f3cb4bf},

doi = {10.1093/nar/gkad430},

issn = {03051048},

year  = {2023},

date = {2023-01-01},

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: 14; All Open Access, Gold Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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=10.1093%2fbioinformatics%2fbtad260\&partnerID=40\&md5=39b2bf96d22ea0ee520b95f47b590984},

doi = {10.1093/bioinformatics/btad260},

issn = {13674803},

year  = {2023},

date = {2023-01-01},

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}

}

@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=10.2217%2fepi-2023-0079\&partnerID=40\&md5=5fb586acb83064545e1a62385bf47b83},

doi = {10.2217/epi-2023-0079},

issn = {17501911},

year  = {2023},

date = {2023-01-01},

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: 2},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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. van 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=10.1172%2fJCI165019\&partnerID=40\&md5=0f32fc96f0219379d9b830efbbbbefb6},

doi = {10.1172/JCI165019},

issn = {00219738},

year  = {2023},

date = {2023-01-01},

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}

}

@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 Lionel Breuza and Cristina Casals-Casas and Elisabeth Coudert and Anne Estreicher and Maria Livia Famiglietti and Arnaud Gos and Nadine Gruaz-Gumowski and Chantal Hulo and Florence Jungo and Philippe Le Mercier and Damien Lieberherr and Patrick Masson and Ivo Pedruzzi and Lucille Pourcel and Sylvain Poux and Catherine Rivoire and Shyamala Sundaram and Alex Bateman and Emily Bowler-Barnett and Hema Bye-A-Jee and Paul Denny and Alexandr Ignatchenko and Rizwan Ishtiaq and Antonia Lock and Yvonne Lussi and Michele Magrane and Maria J. Martin and Sandra Orchard and Pedro Raposo and Elena Speretta and Nidhi Tyagi and Kate Warner and Rossana Zaru and Alexander D. Diehl and Juancarlos Chan and Stavros Diamantakis and Daniela Raciti and Magdalena Zarowiecki and Malcolm Fisher and Christina James-Zorn and Virgilio Ponferrada and Aaron Zorn and Sridhar Ramachandran and Leyla Ruzicka and Monte Westerfield},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85164785564\&doi=10.1093%2fgenetics%2fiyad031\&partnerID=40\&md5=d315a8c84634510d971d9d805f26769d},

doi = {10.1093/genetics/iyad031},

issn = {00166731},

year  = {2023},

date = {2023-01-01},

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: 515; All Open Access, Hybrid Gold Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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=10.1038%2fs41592-023-01915-x\&partnerID=40\&md5=af65986826866a6ce2801c43a3d9d29a},

doi = {10.1038/s41592-023-01915-x},

issn = {15487091},

year  = {2023},

date = {2023-01-01},

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}

}

@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=10.1093%2fnar%2fgkad214\&partnerID=40\&md5=732e97008f88abbbfa755ec7a4fa1ee6},

doi = {10.1093/nar/gkad214},

issn = {03051048},

year  = {2023},

date = {2023-01-01},

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: 6; All Open Access, Gold Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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=10.1016%2fj.jsb.2023.108023\&partnerID=40\&md5=193df29b5c5687ec816f2b9142ae876a},

doi = {10.1016/j.jsb.2023.108023},

issn = {10478477},

year  = {2023},

date = {2023-01-01},

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: 2; All Open Access, Hybrid Gold Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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=10.1038%2fs41431-022-01233-4\&partnerID=40\&md5=56692e2c9b3994a0703776134808e698},

doi = {10.1038/s41431-022-01233-4},

issn = {10184813},

year  = {2023},

date = {2023-01-01},

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}

}

@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=10.1002%2fpro.4655\&partnerID=40\&md5=8bb4b0ffc634a32f0fc5fdf14ab4245f},

doi = {10.1002/pro.4655},

issn = {09618368},

year  = {2023},

date = {2023-01-01},

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}

}

@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=10.1093%2fnar%2fgkac993\&partnerID=40\&md5=e46875f1af4e31a9a0b5bb0276e7a3a5},

doi = {10.1093/nar/gkac993},

issn = {03051048},

year  = {2023},

date = {2023-01-01},

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: 861; All Open Access, Gold Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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=10.1186%2fs13073-022-01064-4\&partnerID=40\&md5=81531c1a0244ddf38e75235cde81e258},

doi = {10.1186/s13073-022-01064-4},

issn = {1756994X},

year  = {2022},

date = {2022-01-01},

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: 7; All Open Access, Gold Open Access, Green Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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=10.1093%2fnar%2fgkab988\&partnerID=40\&md5=9538f59308b4225433abd082b649630b},

doi = {10.1093/nar/gkab988},

issn = {03051048},

year  = {2022},

date = {2022-01-01},

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: 48; All Open Access, Gold Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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=10.3390%2fcancers14041009\&partnerID=40\&md5=a1ec0d6bae3dd398c489f828c58a9d04},

doi = {10.3390/cancers14041009},

issn = {20726694},

year  = {2022},

date = {2022-01-01},

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}

}

@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=10.1002%2fpro.4466\&partnerID=40\&md5=8fac8ca44f3f4c34e62c585165baa7dc},

doi = {10.1002/pro.4466},

issn = {09618368},

year  = {2022},

date = {2022-01-01},

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: 42; All Open Access, Hybrid Gold Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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=10.1093%2fnar%2fgkab1060\&partnerID=40\&md5=4987bea33a75620f0883d6e23e5a026e},

doi = {10.1093/nar/gkab1060},

issn = {03051048},

year  = {2022},

date = {2022-01-01},

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: 30; All Open Access, Gold Open Access, Green Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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=10.1002%2fcpz1.484\&partnerID=40\&md5=c0b162170006c7f2db3710e8b52eef9b},

doi = {10.1002/cpz1.484},

issn = {26911299},

year  = {2022},

date = {2022-01-01},

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}

}

@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=10.1093%2fbioinformatics%2fbtac521\&partnerID=40\&md5=4d6f26134afd4ec6aa8b90a9c55bd40c},

doi = {10.1093/bioinformatics/btac521},

issn = {13674803},

year  = {2022},

date = {2022-01-01},

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}

}

@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=10.1093%2fnar%2fgkab1082\&partnerID=40\&md5=270bf5618598238b9e614e8070e3723a},

doi = {10.1093/nar/gkab1082},

issn = {03051048},

year  = {2022},

date = {2022-01-01},

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 30%. 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: 107; All Open Access, Gold Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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=10.1093%2fbioinformatics%2fbtab764\&partnerID=40\&md5=c8c0d4a29d86a08880a568a5b8eac3bb},

doi = {10.1093/bioinformatics/btab764},

issn = {13674803},

year  = {2022},

date = {2022-01-01},

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}

}

@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=10.3390%2fbiom12010092\&partnerID=40\&md5=68363b8c137547c19a70094b1da39526},

doi = {10.3390/biom12010092},

issn = {2218273X},

year  = {2022},

date = {2022-01-01},

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}

}

@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=10.1001%2fjamanetworkopen.2021.41911\&partnerID=40\&md5=32c9ffb6cf9d94db2d9f3bd72f534d93},

doi = {10.1001/jamanetworkopen.2021.41911},

issn = {25743805},

year  = {2022},

date = {2022-01-01},

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 (51.4%) in the PWS group, 20 patients (45.5%) in the AS group, and 6 patients (66.7%) in the Dup15q group who had sex reported were male. The validation data set showed MS-QMA sensitivity of 99.0% for PWS, 93.8% for AS, and 77.8% for Dup15q; specificity of 100% for PWS, AS, and Dup15q; positive predictive and negative predictive values of 100% for PWS and AS; and a positive predictive value of 87.5% and negative predictive value of 100% 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 67.0% for AS, 33.0% for PWS, and 44.0% 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: 16; All Open Access, Gold Open Access, Green Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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=10.1093%2fnar%2fgkac365\&partnerID=40\&md5=b97a49e2ca7e88f01ad20ecc84f3780a},

doi = {10.1093/nar/gkac365},

issn = {03051048},

year  = {2022},

date = {2022-01-01},

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: 78; All Open Access, Gold Open Access, Green Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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=10.1093%2fnar%2fgkac386\&partnerID=40\&md5=293978de7e452d8cb9f59ca16ea93afb},

doi = {10.1093/nar/gkac386},

issn = {03051048},

year  = {2022},

date = {2022-01-01},

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: 54; All Open Access, Gold Open Access, Green Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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=10.1093%2fnar%2fgkab1025\&partnerID=40\&md5=1c0f0bace596f47b96e7fc69267329dc},

doi = {10.1093/nar/gkab1025},

issn = {03051048},

year  = {2022},

date = {2022-01-01},

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}

}

@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=10.1093%2fbioinformatics%2fbtac627\&partnerID=40\&md5=ee4d714dba468725c6c3ccc7dbf78bb4},

doi = {10.1093/bioinformatics/btac627},

issn = {13674803},

year  = {2022},

date = {2022-01-01},

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}

}

@article{Varadi2022,

title = {3D-Beacons: Decreasing the gap between protein sequences and structures through a federated network of protein structure data resources},

author = { Mihaly Varadi and Sreenath Nair and Ian Sillitoe and Gerardo Tauriello and Stephen Anyango and Stefan Bienert and Clemente Borges and Mandar Deshpande and Tim Green and Demis Hassabis and Andras Hatos and Tamas Hegedus and Maarten L Hekkelman and Robbie Joosten and John Jumper and Agata Laydon and Dmitry Molodenskiy and Damiano Piovesan and Edoardo Salladini and Steven L Salzberg and Markus J Sommer and Martin Steinegger and Erzsebet Suhajda and Dmitri Svergun and Luiggi Tenorio-Ku and Silvio Tosatto and Kathryn Tunyasuvunakool and Andrew Mark Waterhouse and Augustin Z\'{i}dek and Torsten Schwede and Christine Orengo and Sameer Velankar},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85143181019\&doi=10.1093%2fgigascience%2fgiac118\&partnerID=40\&md5=dfed4704c49e7d2e74567a6f836f6dad},

doi = {10.1093/gigascience/giac118},

issn = {2047217X},

year  = {2022},

date = {2022-01-01},

abstract = {While scientists can often infer the biological function of proteins from their 3-dimensional quaternary structures, the gap between the number of known protein sequences and their experimentally determined structures keeps increasing. A potential solution to this problem is presented by ever more sophisticated computational protein modeling approaches. While often powerful on their own, most methods have strengths and weaknesses. Therefore, it benefits researchers to examine models from various model providers and perform comparative analysis to identify what models can best address their specific use cases. To make data from a large array of model providers more easily accessible to the broader scientific community, we established 3D-Beacons, a collaborative initiative to create a federated network with unified data access mechanisms. The 3D-Beacons Network allows researchers to collate coordinate files and metadata for experimentally determined and theoretical protein models from state-of-The-Art and specialist model providers and also from the Protein Data Bank. © 2022 The Author(s). Published by Oxford University Press GigaScience.},

note = {Cited by: 13; All Open Access, Green Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Fusto2022,

title = {Expanding the clinical-pathological and genetic spectrum of RYR1-related congenital myopathies with cores and minicores: an Italian population study},

author = { Aurora Fusto and Denise Cassandrini and Chiara Fiorillo and Valentina Codemo and Guja Astrea and Adele D’Amico and Lorenzo Maggi and Francesca Magri and Marika Pane and Giorgio Tasca and Daniele Sabbatini and Luca Bello and Roberta Battini and Pia Bernasconi and Fabiana Fattori and Enrico Silvio Bertini and Giacomo Comi and Sonia Messina and Tiziana Mongini and Isabella Moroni and Chiara Panicucci and Angela Berardinelli and Alice Donati and Vincenzo Nigro and Antonella Pini and Melania Giannotta and Claudia Dosi and Enzo Ricci and Eugenio Mercuri and Giovanni Minervini and Silvio Tosatto and Filippo Santorelli and Claudio Bruno and Elena Pegoraro},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85128316270\&doi=10.1186%2fs40478-022-01357-0\&partnerID=40\&md5=f45e114e5bbbb8609c97f49b53b08397},

doi = {10.1186/s40478-022-01357-0},

issn = {20515960},

year  = {2022},

date = {2022-01-01},

abstract = {Mutations in the RYR1 gene, encoding ryanodine receptor 1 (RyR1), are a well-known cause of Central Core Disease (CCD) and Multi-minicore Disease (MmD). We screened a cohort of 153 patients carrying an histopathological diagnosis of core myopathy (cores and minicores) for RYR1 mutation. At least one RYR1 mutation was identified in 69 of them and these patients were further studied. Clinical and histopathological features were collected. Clinical phenotype was highly heterogeneous ranging from asymptomatic or paucisymptomatic hyperCKemia to severe muscle weakness and skeletal deformity with loss of ambulation. Sixty-eight RYR1 mutations, generally missense, were identified, of which 16 were novel. The combined analysis of the clinical presentation, disease progression and the structural bioinformatic analyses of RYR1 allowed to associate some phenotypes to mutations in specific domains. In addition, this study highlighted the structural bioinformatics potential in the prediction of the pathogenicity of RYR1 mutations. Further improvement in the comprehension of genotype\textendashphenotype relationship of core myopathies can be expected in the next future: the actual lack of the human RyR1 crystal structure paired with the presence of large intrinsically disordered regions in RyR1, and the frequent presence of more than one RYR1 mutation in core myopathy patients, require designing novel investigation strategies to completely address RyR1 mutation effect. © 2022, The Author(s).},

note = {Cited by: 8; All Open Access, Gold Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Piovesan2022144,

title = {Databases for intrinsically disordered proteins},

author = { Damiano Piovesan and Alexander Miguel Monzon and Federica Quaglia and Silvio C. E. Tosatto},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85123972941\&doi=10.1107%2fS2059798321012109\&partnerID=40\&md5=fc97d8245c35d1b0c65faa617398ca2e},

doi = {10.1107/S2059798321012109},

issn = {20597983},

year  = {2022},

date = {2022-01-01},

abstract = {Intrinsically disordered regions (IDRs) lacking a fixed three-dimensional protein structure are widespread and play a central role in cell regulation. Only a small fraction of IDRs have been functionally characterized, with heterogeneous experimental evidence that is largely buried in the literature. Predictions of IDRs are still difficult to estimate and are poorly characterized. Here, an overview of the publicly available knowledge about IDRs is reported, including manually curated resources, deposition databases and prediction repositories. The types, scopes and availability of the various resources are analyzed, and their complementarity and overlap are highlighted. The volume of information included and the relevance to the field of structural biology are compared. © 2022.},

note = {Cited by: 8; All Open Access, Green Open Access, Hybrid Gold Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Catoni2022,

title = {Investigating the Retained Inhibitory Effect of Cobimetinib against p.P124L Mutated MEK1: A Combined Liquid Biopsy and in Silico Approach},

author = { Cristina Catoni and Cristina Poggiana and Antonella Facchinetti and Jacopo Pigozzo and Luisa Piccin and Vanna Chiarion-Sileni and Antonio Rosato and Giovanni Minervini and Maria Chiara Scaini},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85137888553\&doi=10.3390%2fcancers14174153\&partnerID=40\&md5=97bebd411d8498591f1c8cf1320c09fe},

doi = {10.3390/cancers14174153},

issn = {20726694},

year  = {2022},

date = {2022-01-01},

abstract = {The systemic treatment of metastatic melanoma has radically changed, due to an improvement in the understanding of its genetic landscape and the advent of targeted therapy. However, the response to BRAF/MEK inhibitors is transitory, and big efforts were made to identify the mechanisms underlying the resistance. We exploited a combined approach, encompassing liquid biopsy analysis and molecular dynamics simulation, for tracking tumor evolution, and in parallel defining the best treatment option. The samples at different time points were collected from a BRAF-mutant melanoma patient who developed an early resistance to dabrafenib/trametinib. The analysis of the circulating tumor DNA (ctDNA) identified the MEK1 p.P124L mutation that confers resistance to trametinib. With an in silico modeling, we identified cobimetinib as an alternative MEK inhibitor, and consequently suggested a therapy switch to vemurafenib/cobimetinib. The patient response was followed by ctDNA tracking and circulating melanoma cell (CMC) count. The cobimetinib administration led to an important reduction in the BRAF p.V600E and MEK1 p.P124L allele fractions and in the CMC number, features suggestive of a putative response. In summary, this study emphasizes the usefulness of a liquid biopsy-based approach combined with in silico simulation, to track real-time tumor evolution while assessing the best treatment option. © 2022 by the authors.},

note = {Cited by: 4; All Open Access, Gold Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Paladin2021D452,

title = {RepeatsDB in 2021: Improved data and extended classification for protein tandem repeat structures},

author = { Lisanna Paladin and Martina Bevilacqua and Sara Errigo and Damiano Piovesan and Ivan Mi\v{c}eti\'{c} and Marco Necci and Alexander Miguel Monzon and Maria Laura Fabre and Jose Luis Lopez and Juliet F. Nilsson and Javier Rios and Pablo Lorenzano Menna and Maia Cabrera and Martin Gonzalez Buitron and Mariane Gon\c{c}alves Kulik and Sebastian Fernandez-Alberti and Maria Silvina Fornasari and Gustavo Parisi and Antonio Lagares and Layla Hirsh and Miguel A. Andrade-Navarro and Andrey V. Kajava and Silvio C.E. Tosatto},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85099429028\&doi=10.1093%2fnar%2fgkaa1097\&partnerID=40\&md5=9a76417ee8612b9b07dd285c326e9b92},

doi = {10.1093/nar/gkaa1097},

issn = {03051048},

year  = {2021},

date = {2021-01-01},

abstract = {The RepeatsDB database (URL: https://repeatsdb.org/) provides annotations and classification for protein tandem repeat structures from the Protein Data Bank (PDB). Protein tandem repeats are ubiquitous in all branches of the tree of life. The accumulation of solved repeat structures provides new possibilities for classification and detection, but also increasing the need for annotation. Here we present RepeatsDB 3.0, which addresses these challenges and presents an extended classification scheme. The major conceptual change compared to the previous version is the hierarchical classification combining top levels based solely on structural similarity (Class \> Topology \> Fold) with two new levels (Clan \> Family) requiring sequence similarity and describing repeat motifs in collaboration with Pfam. Data growth has been addressed with improved mechanisms for browsing the classification hierarchy. A new UniProt-centric view unifies the increasingly frequent annotation of structures from identical or similar sequences. This update of RepeatsDB aligns with our commitment to develop a resource that extracts, organizes and distributes specialized information on tandem repeat protein structures. © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.},

note = {Cited by: 30; All Open Access, Gold Open Access, Green Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bertolio2021,

title = {A Novel Splice Variant of Human TGF-β Type II Receptor Encodes a Soluble Protein and Its Fc-Tagged Version Prevents Liver Fibrosis in vivo},

author = { Marcela Soledad Bertolio and Anabela La Colla and Alejandra Carrea and Ana Romo and Gabriela Canziani and Stella Maris Echarte and Sabrina Campisano and German Patricio Barletta and Alexander Miguel Monzon and Tania Melina Rodr\'{i}guez and Andrea Nancy Chisari and Ricardo Alfredo Dewey},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85115828696\&doi=10.3389%2ffcell.2021.690397\&partnerID=40\&md5=26e5f138dcc93d1195f8a2ee8232f853},

doi = {10.3389/fcell.2021.690397},

issn = {2296634X},

year  = {2021},

date = {2021-01-01},

abstract = {We describe, for the first time, a new splice variant of the human TGF-β type II receptor (TβRII). The new transcript lacks 149 nucleotides, resulting in a frameshift and the emergence of an early stop codon, rendering a truncated mature protein of 57 amino acids. The predicted protein, lacking the transmembrane domain and with a distinctive 13-amino-acid stretch at its C-terminus, was named TβRII-Soluble Endogenous (TβRII-SE). Binding predictions indicate that the novel 13-amino-acid stretch interacts with all three TGF-β cognate ligands and generates a more extensive protein\textendashprotein interface than TβRII. TβRII-SE and human IgG1 Fc domain were fused in frame in a lentiviral vector (Lv) for further characterization. With this vector, we transduced 293T cells and purified TβRII-SE/Fc by A/G protein chromatography from conditioned medium. Immunoblotting revealed homogeneous bands of approximately 37 kDa (reduced) and 75 kDa (non-reduced), indicating that TβRII-SE/Fc is secreted as a disulfide-linked homodimer. Moreover, high-affinity binding of TβRII-SE to the three TGF-β isoforms was confirmed by surface plasmon resonance (SPR) analysis. Also, intrahepatic delivery of Lv.TβRII-SE/Fc in a carbon tetrachloride-induced liver fibrosis model revealed amelioration of liver injury and fibrosis. Our results indicate that TβRII-SE is a novel member of the TGF-β signaling pathway with distinctive characteristics. This novel protein offers an alternative for the prevention and treatment of pathologies caused by the overproduction of TGF-β ligands. © Copyright © 2021 Bertolio, La Colla, Carrea, Romo, Canziani, Echarte, Campisano, Barletta, Monzon, Rodr\'{i}guez, Chisari and Dewey.},

note = {Cited by: 2; All Open Access, Gold Open Access, Green Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}