@article{SCOPUS_ID:85213041340,

title = {Searching and Using MobiDB Resource 6 to Explore Predictions and Annotations for Intrinsically Disordered Proteins},

author = {Maria Cristina Aspromonte and Federica Quaglia and Alexander Miguel Monzon and Damiano Clementel and Alessio Del Conte and Damiano Piovesan and Silvio C. E. Tosatto},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-85213041340&origin=inward},

doi = {10.1002/cpz1.70077},

year  = {2024},

date = {2024-01-01},

journal = {Current Protocols},

volume = {4},

number = {12},

publisher = {John Wiley and Sons Inc},

abstract = {Current Protocols© 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC.Intrinsically disordered proteins (IDPs) make up around 30% of eukaryotic proteomes and play a crucial role in cellular processes and in pathological conditions such as neurodegenerative disorders and cancers. However, IDPs exhibit dynamic conformational ensembles and are often involved in the formation of biomolecular condensates. Understanding the function of IDPs is critical to research in many areas of science. MobiDB is a unique resource that serves as a comprehensive knowledgebase of IDPs and intrinsically disordered regions (IDRs), combining disorder annotations from experimental evidence and predictions for a broad range of protein sequences. Over the past decade, MobiDB has evolved with a focus on expanding annotation coverage, standardizing annotation provenance, and enhancing database accessibility. The latest MobiDB, version 6, released in July 2024, includes significant improvements, such as the integration of AlphaFoldDB predictions and a new homology transfer pipeline that has substantially increased the number of entries with high-quality annotations. The user interface has also been updated, highlighting annotation features, clarifying the entry page, and providing an immediate overview of disorder, binding, and disorder functions information in the protein sequence. This protocol guides the user through applications of the MobiDB, including disorder prediction, curated data analysis, and exploration of interaction data. This guide covers how to perform a search in MobiDB annotations using the web interface and the MobiDB REST API for programmatic access. The protocols use a step-by-step walkthrough using the human growth hormone receptor to demonstrate MobiDB's functions for visualization and interpretation of protein disorder data. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Searching MobiDB query formats. Basic Protocol 2: Searching MobiDB selected datasets and selected proteomes. Basic Protocol 3: Performing a search on the Statistics page in MobiDB. Support Protocol: Programmatic access with MobiDB REST API. Basic Protocol 4: Visualizing and interpreting a MobiDB Entry: The GHR use case.},

note = {Cited by: 0; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:85176208048,

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 Erzsébet Fichó and Galo E. Balatti and Gustavo Parisi and Martín González Buitrón and Gabor Erdos and Matyas Pajkos and Zsuzsanna Dosztányi 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 Zsófia Kálmán and Juliet F. Nilsson and Jaime Santos and Carlos Pintado-Grima and Salvador Ventura and Veronika Ács and Rita Pancsa and Mariane Goncalves Kulik and Miguel A. Andrade-Navarro and Pedro José Barbosa Pereira and Sonia Longhi and Philippe Le Mercier and Julian Bergier and Peter Tompa and Tamas Lazar},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-85176208048&origin=inward},

doi = {10.1093/nar/gkad928},

year  = {2024},

date = {2024-01-01},

journal = {Nucleic Acids Research},

volume = {52},

number = {D1},

pages = {D434-D441},

publisher = {Oxford University Press},

abstract = {© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.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.},

note = {Cited by: 38; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:85145966264,

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/record/display.uri?eid=2-s2.0-85145966264&origin=inward},

doi = {10.1093/nar/gkac1065},

year  = {2023},

date = {2023-01-01},

journal = {Nucleic Acids Research},

volume = {51},

number = {1 D},

pages = {D438-D444},

publisher = {Oxford University Press},

abstract = {© 2023 The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.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.},

note = {Cited by: 82; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:85164785564,

title = {The Gene Ontology knowledgebase in 2023},

author = {Suzi A. Aleksander and James Balhoff and Seth Carbon and J. Michael Cherry and Harold J. Drabkin and Dustin Ebert and Marc Feuermann and Pascale Gaudet and Nomi L. Harris and David P. Hill and Raymond Lee and Huaiyu Mi and Sierra Moxon and Christopher J. Mungall and Anushya Muruganugan and Tremayne Mushayahama and Paul W. Sternberg and Paul D. Thomas and Kimberly Van Auken and Jolene Ramsey and Deborah A. Siegele and Rex L. Chisholm and Petra Fey and Maria Cristina Aspromonte and Maria Victoria Nugnes and Federica Quaglia and Silvio Tosatto and Michelle Giglio and Suvarna Nadendla and Giulia Antonazzo and Helen Attrill and Gil Dos Santos and Steven Marygold and Victor Strelets and Christopher J. Tabone and Jim Thurmond and Pinglei Zhou and Saadullah H. Ahmed and Praoparn Asanitthong and Diana Luna Buitrago and Meltem N. Erdol and Matthew C. Gage and Mohamed Ali Kadhum and Kan Yan Chloe Li and Miao Long and Aleksandra Michalak and Angeline Pesala and Armalya Pritazahra and Shirin C. C. Saverimuttu and Renzhi Su and Kate E. Thurlow and Ruth C Lovering and Colin Logie and Snezhana Oliferenko and Judith Blake and Karen Christie and Lori Corbani and Mary E. Dolan and Li Ni and Dmitry Sitnikov and Cynthia Smith and Alayne Cuzick and James Seager and Laurel Cooper and Justin Elser and Pankaj Jaiswal and Parul Gupta and Sushma Naithani and Manuel Lera-Ramirez and Kim Rutherford and Valerie Wood and Jeffrey L. De Pons and Melinda R. Dwinell and G. Thomas Hayman and Mary L. Kaldunski and Anne E. Kwitek and Stanley J. F. Laulederkind and Marek A. Tutaj and Mahima Vedi and Shur-Jen Wang and Peter D'Eustachio and Lucila Aimo and Kristian Axelsen and Alan Bridge and Nevila Hyka-Nouspikel and Anne Morgat and Stacia R. Engel and Kalpana Karra and Stuart R. Miyasato and Robert S. Nash and Marek S. Skrzypek and Shuai Weng and Edith D. Wong and Erika Bakker and Tanya Z. Berardini and Leonore Reiser and Andrea Auchincloss and Ghislaine Argoud-Puy and Marie-Claude Blatter and Emmanuel Boutet and ...},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-85164785564&origin=inward},

doi = {10.1093/genetics/iyad031},

year  = {2023},

date = {2023-01-01},

journal = {Genetics},

volume = {224},

number = {1},

publisher = {Oxford University Press},

abstract = {© 2023 The Author(s). Published by Oxford University Press on behalf of The Genetics Society of America.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.},

note = {Cited by: 943; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SCOPUS_ID:85142646250,

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 Rzońca-Niewczas and Maria Giuseppina Miano and Alessandra Murgia},

url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-85142646250&origin=inward},

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

year  = {2023},

date = {2023-01-01},

journal = {European Journal of Human Genetics},

volume = {31},

number = {2},

pages = {202-215},

publisher = {Springer Nature},

abstract = {© 2022, This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.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.},

note = {Cited by: 11; Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}