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3. Minimum information guidelines for experiments structurally characterizing intrinsically disordered protein regions

Author

Mészáros, Bálint, Hatos, András, Palopoli, Nicolas, Quaglia, Federica, Salladini, Edoardo, Van Roey, Kim, Arthanari, Haribabu, Dosztányi, Zsuzsanna, Felli, Isabella C., Fischer, Patrick D., Hoch, Jeffrey C., Jeffries, Cy M., Longhi, Sonia, Maiani, Emiliano, Orchard, Sandra, Pancsa, Rita, Papaleo, Elena, Pierattelli, Roberta, Piovesan, Damiano, Pritisanac, Iva, Tenorio, Luiggi, Viennet, Thibault, Tompa, Peter, Vranken, Wim, Tosatto, Silvio C. E., and Davey, Norman E.

Published
2023
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4. List of contributors

Author

Bhowmick, Jayantika, primary, Brocca, Stefania, additional, Cascarina, Sean M., additional, Chandra, Soumyanetra, additional, Chen, Limin, additional, Davé, Vrushank, additional, Di Bartolo, Ary Lautaro, additional, Dosztányi, Zsuzsanna, additional, Drake, Justin A., additional, Erdős, Gábor, additional, Gondelaud, Frank, additional, Graham, Kristin D., additional, Grandori, Rita, additional, Gupta, Munishwar Nath, additional, Harrison, Paul M., additional, Huang, Qiaojing, additional, Lai, Luhua, additional, Liu, Zhirong, additional, Longhi, Sonia, additional, Masone, Diego, additional, Natalello, Antonino, additional, Pettitt, B. Montgomery, additional, Ross, Eric D., additional, Santambrogio, Carlo, additional, Schramm, Antoine, additional, Stachowiak, Jeanne C., additional, Uversky, Vladimir N., additional, Varadarajan, Raghavan, additional, Workman, Riley J., additional, Yuan, Feng, additional, and Zeno, Wade F., additional

Published
2023
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6. ViralPrimer: a web server to monitor viral nucleic acid amplification tests' primer efficiency during pandemics, with emphasis on SARS-CoV-2 and Mpox.

Author

Deutsch, Norbert, Dosztányi, Zsuzsanna, Csabai, István, Medgyes-Horváth, Anna, Pipek, Orsolya Anna, Stéger, József, Papp, Krisztián, Visontai, Dávid, Erdős, Gábor, and Mentes, Anikó

Subjects
*NUCLEIC acid amplification techniques, *DATABASES, *MONKEYPOX, *NUCLEOTIDE sequencing, *SARS-CoV-2, *INTERNET servers
Abstract

Summary Accurate pathogen identification is crucial during outbreaks, especially with the emergence of new variants requiring frequent primer updates. However, resources for maintaining up-to-date verification of primer sequences are often limited, which poses challenges for reliable diagnosis and hinders potential monitoring efforts based on genome sequencing. To address this, we introduce ViralPrimer, a web server facilitating primer design, SARS-CoV-2 and Mpox variant monitoring, and adaptation to future threats. ViralPrimer aims to enhance diagnostic accuracy with its comprehensive primer database, mutation analysis assistance, and user primer upload feature. Its adaptable design allows monitoring of other rapidly mutating pathogens, contributing to broader public health protection efforts. Availability and implementation ViralPrimer is freely accessible and open to all users with no login requirement at https://viralprimer.elte.hu/. The application is hosted on a DJANGO v3.2.13 web server, with a PostgreSQL database, and the frontend was implemented using jQuery v3.6.0, vanilla JavaScript vES6, and Bootstrap v5.1. [ABSTRACT FROM AUTHOR]

Published
2024
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11. InterPro in 2017—beyond protein family and domain annotations

Author

Finn, Robert D, Attwood, Teresa K, Babbitt, Patricia C, Bateman, Alex, Bork, Peer, Bridge, Alan J, Chang, Hsin-Yu, Dosztányi, Zsuzsanna, El-Gebali, Sara, Fraser, Matthew, Gough, Julian, Haft, David, Holliday, Gemma L, Huang, Hongzhan, Huang, Xiaosong, Letunic, Ivica, Lopez, Rodrigo, Lu, Shennan, Marchler-Bauer, Aron, Mi, Huaiyu, Mistry, Jaina, Natale, Darren A, Necci, Marco, Nuka, Gift, Orengo, Christine A, Park, Youngmi, Pesseat, Sebastien, Piovesan, Damiano, Potter, Simon C, Rawlings, Neil D, Redaschi, Nicole, Richardson, Lorna, Rivoire, Catherine, Sangrador-Vegas, Amaia, Sigrist, Christian, Sillitoe, Ian, Smithers, Ben, Squizzato, Silvano, Sutton, Granger, Thanki, Narmada, Thomas, Paul D, Tosatto, Silvio CE, Wu, Cathy H, Xenarios, Ioannis, Yeh, Lai-Su, Young, Siew-Yit, and Mitchell, Alex L

Subjects
Generic health relevance, Computational Biology, Databases, Protein, Humans, Molecular Sequence Annotation, Phylogeny, Protein Interaction Domains and Motifs, Software, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Developmental Biology
Abstract

InterPro (http://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and to predict the presence of important domains and sites. InterProScan is the underlying software that allows both protein and nucleic acid sequences to be searched against InterPro's predictive models, which are provided by its member databases. Here, we report recent developments with InterPro and its associated software, including the addition of two new databases (SFLD and CDD), and the functionality to include residue-level annotation and prediction of intrinsic disorder. These developments enrich the annotations provided by InterPro, increase the overall number of residues annotated and allow more specific functional inferences.

Published
2017

17. Acetylation of nuclear receptors in health and disease: an update.

Author

Ashton, Anthony W., Dhanjal, Harpreet K., Rossner, Benjamin, Mahmood, Huma, Patel, Vivek I., Nadim, Mohammad, Lota, Manpreet, Shahid, Farhan, Li, Zhiping, Joyce, David, Pajkos, Matyas, Dosztányi, Zsuzsanna, Jiao, Xuanmao, and Pestell, Richard G.

Subjects
POST-translational modification, ACETYLATION, HOMEOSTASIS, HUMAN reproduction, ANDROGEN receptors, GENE expression
Abstract

Lysine acetylation is a common reversible post‐translational modification of proteins that plays a key role in regulating gene expression. Nuclear receptors (NRs) include ligand‐inducible transcription factors and orphan receptors for which the ligand is undetermined, which together regulate the expression of genes involved in development, metabolism, homeostasis, reproduction and human diseases including cancer. Since the original finding that the ERα, AR and HNF4 are acetylated, we now understand that the vast majority of NRs are acetylated and that this modification has profound effects on NR function. Acetylation sites are often conserved and involve both ordered and disordered regions of NRs. The acetylated residues function as part of an intramolecular signalling platform intersecting phosphorylation, methylation and other modifications. Acetylation of NR has been shown to impact recruitment into chromatin, co‐repressor and coactivator complex formation, sensitivity and specificity of regulation by ligand and ligand antagonists, DNA binding, subcellular distribution and transcriptional activity. A growing body of evidence in mice indicates a vital role for NR acetylation in metabolism. Additionally, mutations of the NR acetylation site occur in human disease. This review focuses on the role of NR acetylation in coordinating signalling in normal physiology and disease. [ABSTRACT FROM AUTHOR]

Published
2024
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21. Acetylation of nuclear receptors in health and disease: an update

Author

Ashton, Anthony W., primary, Dhanjal, Harpreet K., additional, Rossner, Benjamin, additional, Mahmood, Huma, additional, Patel, Vivek I., additional, Nadim, Mohammad, additional, Lota, Manpreet, additional, Shahid, Farhan, additional, Li, Zhiping, additional, Joyce, David, additional, Pajkos, Matyas, additional, Dosztányi, Zsuzsanna, additional, Jiao, Xuanmao, additional, and Pestell, Richard G., additional

Published
2022
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26. MIADE metadata guidelines: Minimum Information About a Disorder Experiment

Author

Mészáros, Bálint, primary, Hatos, András, additional, Palopoli, Nicolas, additional, Quaglia, Federica, additional, Salladini, Edoardo, additional, Van Roey, Kim, additional, Arthanari, Haribabu, additional, Dosztányi, Zsuzsanna, additional, Felli, Isabella C., additional, Fischer, Patrick D, additional, Hoch, Jeffrey C., additional, Jeffries, Cy M, additional, Longhi, Sonia, additional, Maiani, Emiliano, additional, Orchard, Sandra, additional, Pancsa, Rita, additional, Papaleo, Elena, additional, Pierattelli, Roberta, additional, Piovesan, Damiano, additional, Pritisanac, Iva, additional, Viennet, Thibault, additional, Tompa, Peter, additional, Vranken, Wim, additional, Tosatto, Silvio CE, additional, and Davey, Norman E, additional

Published
2022
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27. DisProt in 2022 : improved quality and accessibility of protein intrinsic disorder annotation

Author

Quaglia, Federica, Mészáros, Bálint, Salladini, Edoardo, Hatos, András, Pancsa, Rita, Chemes, Lucía B., Pajkos, Mátyás, Lazar, Tamas, Peña-Díaz, Samuel, Santos, Jaime, Ács, Veronika, Farahi, Nazanin, Fichó, Erzsébet, Aspromonte, Maria Cristina, Bassot, Claudio, Chasapi, Anastasia, Davey, Norman E., Davidović, Radoslav, Dobson, Laszlo, Elofsson, Arne, Erdős, Gábor, Gaudet, Pascale, Giglio, Michelle, Glavina, Juliana, Iserte, Javier, Iglesias, Valentín, Kálmán, Zsófia, Lambrughi, Matteo, Leonardi, Emanuela, Longhi, Sonia, Macedo-Ribeiro, Sandra, Maiani, Emiliano, Marchetti, Julia, Marino-Buslje, Cristina, Mészáros, Attila, Monzon, Alexander Miguel, Minervini, Giovanni, Nadendla, Suvarna, Nilsson, Juliet F., Novotný, Marian, Ouzounis, Christos A., Palopoli, Nicolás, Papaleo, Elena, Barbosa Pereira, Pedro José, Pozzati, Gabriele, Promponas, Vasilis J., Pujols, Jordi, Sanchez Rocha, Alma Carolina, Salas, Martin, Rodriguez Sawicki, Luciana, Schad, Eva, Shenoy, Aditi, Szaniszló, Tamás, Tsirigos, Konstantinos D., Veljkovic, Nevena, Parisi, Gustavo, Ventura, Salvador, Dosztányi, Zsuzsanna, Tompa, Peter, Tosatto, Silvio C. E., Piovesan, Damiano, Quaglia, Federica, Mészáros, Bálint, Salladini, Edoardo, Hatos, András, Pancsa, Rita, Chemes, Lucía B., Pajkos, Mátyás, Lazar, Tamas, Peña-Díaz, Samuel, Santos, Jaime, Ács, Veronika, Farahi, Nazanin, Fichó, Erzsébet, Aspromonte, Maria Cristina, Bassot, Claudio, Chasapi, Anastasia, Davey, Norman E., Davidović, Radoslav, Dobson, Laszlo, Elofsson, Arne, Erdős, Gábor, Gaudet, Pascale, Giglio, Michelle, Glavina, Juliana, Iserte, Javier, Iglesias, Valentín, Kálmán, Zsófia, Lambrughi, Matteo, Leonardi, Emanuela, Longhi, Sonia, Macedo-Ribeiro, Sandra, Maiani, Emiliano, Marchetti, Julia, Marino-Buslje, Cristina, Mészáros, Attila, Monzon, Alexander Miguel, Minervini, Giovanni, Nadendla, Suvarna, Nilsson, Juliet F., Novotný, Marian, Ouzounis, Christos A., Palopoli, Nicolás, Papaleo, Elena, Barbosa Pereira, Pedro José, Pozzati, Gabriele, Promponas, Vasilis J., Pujols, Jordi, Sanchez Rocha, Alma Carolina, Salas, Martin, Rodriguez Sawicki, Luciana, Schad, Eva, Shenoy, Aditi, Szaniszló, Tamás, Tsirigos, Konstantinos D., Veljkovic, Nevena, Parisi, Gustavo, Ventura, Salvador, Dosztányi, Zsuzsanna, Tompa, Peter, Tosatto, Silvio C. E., and Piovesan, Damiano

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.

Published
2022
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28. DisCanVis: Visualizing integrated structural and functional annotations to better understand the effect of cancer mutations located within disordered proteins.

Author

Deutsch, Norbert, Pajkos, Mátyás, Erdős, Gábor, and Dosztányi, Zsuzsanna

Abstract

Intrinsically disordered proteins (IDPs) play important roles in a wide range of biological processes and have been associated with various diseases, including cancer. In the last few years, cancer genome projects have systematically collected genetic variations underlying multiple cancer types. In parallel, the number and different types of disordered proteins characterized by experimental methods have also significantly increased. Nevertheless, the role of IDPs in various types of cancer is still not well understood. In this work, we present DisCanVis, a novel visualization tool for cancer mutations with a special focus on IDPs. In order to aid the interpretation of observed mutations, genome level information is combined with information about the structural and functional properties of proteins. The web server enables users to inspect individual proteins, collect examples with existing annotations of protein disorder and associated function or to discover currently uncharacterized examples with likely disease relevance. Through a REST API interface and precompiled tables the analysis can be extended to a group of proteins. [ABSTRACT FROM AUTHOR]

Published
2023
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29. DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation

Author

Quaglia, Federica, primary, Mészáros, Bálint, additional, Salladini, Edoardo, additional, Hatos, András, additional, Pancsa, Rita, additional, Chemes, Lucía B, additional, Pajkos, Mátyás, additional, Lazar, Tamas, additional, Peña-Díaz, Samuel, additional, Santos, Jaime, additional, Ács, Veronika, additional, Farahi, Nazanin, additional, Fichó, Erzsébet, additional, Aspromonte, Maria Cristina, additional, Bassot, Claudio, additional, Chasapi, Anastasia, additional, Davey, Norman E, additional, Davidović, Radoslav, additional, Dobson, Laszlo, additional, Elofsson, Arne, additional, Erdős, Gábor, additional, Gaudet, Pascale, additional, Giglio, Michelle, additional, Glavina, Juliana, additional, Iserte, Javier, additional, Iglesias, Valentín, additional, Kálmán, Zsófia, additional, Lambrughi, Matteo, additional, Leonardi, Emanuela, additional, Longhi, Sonia, additional, Macedo-Ribeiro, Sandra, additional, Maiani, Emiliano, additional, Marchetti, Julia, additional, Marino-Buslje, Cristina, additional, Mészáros, Attila, additional, Monzon, Alexander Miguel, additional, Minervini, Giovanni, additional, Nadendla, Suvarna, additional, Nilsson, Juliet F, additional, Novotný, Marian, additional, Ouzounis, Christos A, additional, Palopoli, Nicolás, additional, Papaleo, Elena, additional, Pereira, Pedro José Barbosa, additional, Pozzati, Gabriele, additional, Promponas, Vasilis J, additional, Pujols, Jordi, additional, Rocha, Alma Carolina Sanchez, additional, Salas, Martin, additional, Sawicki, Luciana Rodriguez, additional, Schad, Eva, additional, Shenoy, Aditi, additional, Szaniszló, Tamás, additional, Tsirigos, Konstantinos D, additional, Veljkovic, Nevena, additional, Parisi, Gustavo, additional, Ventura, Salvador, additional, Dosztányi, Zsuzsanna, additional, Tompa, Peter, additional, Tosatto, Silvio C E, additional, and Piovesan, Damiano, additional

Published
2021
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31. Critical assessment of protein intrinsic disorder prediction

Author

Necci, Marco, Piovesan, Damiano, Hoque Md, Tamjidul, Walsh, Ian, Iqbal, Sumaiya, Vendruscolo, Michele, Sormanni, Pietro, Wang, Chen, Raimondi, Daniele, Sharma, Ronesh, Zhou, Yaoqi, Litfin, Thomas, Galzitskaya Oxana, Valerianovna, Lobanov Michail, Yu, Vranken, Wim, Wallner, Björn, Mirabello, Claudio, Malhis, Nawar, Dosztányi, Zsuzsanna, Erdős, Gábor, Mészáros, Bálint, Gao, Jianzhao, Wang, Kui, Hu, Gang, Wu, Zhonghua, Sharma, Alok, Hanson, Jack, Paliwal, Kuldip, Callebaut, Isabelle, Bitard-Feildel, Tristan, Orlando, Gabriele, Peng, Zhenling, Xu, Jinbo, Wang, Sheng, Jones David, T., Cozzetto, Domenico, Meng, Fanchi, Yan, Jing, Gsponer, Jörg, Cheng, Jianlin, Wu, Tianqi, Kurgan, Lukasz, Promponas Vasilis, J., Tamana, Stella, Marino-Buslje, Cristina, Martínez-Pérez, Elizabeth, Chasapi, Anastasia, Ouzounis, Christos, Dunker A., Keith, Kajava Andrey, V., Leclercq Jeremy, Y., Aykac-Fas, Burcu, Lambrughi, Matteo, Maiani, Emiliano, Papaleo, Elena, Chemes Lucia, Beatriz, Álvarez, Lucía, González-Foutel Nicolás, S., Iglesias, Valentin, Pujols, Jordi, Ventura, Salvador, Palopoli, Nicolás, Benítez Guillermo, Ignacio, Parisi, Gustavo, Bassot, Claudio, Elofsson, Arne, Govindarajan, Sudha, Lamb, John, Salvatore, Marco, Hatos, András, Monzon Alexander, Miguel, Bevilacqua, Martina, Mičetić, Ivan, Minervini, Giovanni, Paladin, Lisanna, Quaglia, Federica, Leonardi, Emanuela, Davey, Norman, Horvath, Tamas, Kovacs Orsolya, Panna, Murvai, Nikoletta, Pancsa, Rita, Schad, Eva, Szabo, Beata, Tantos, Agnes, Macedo-Ribeiro, Sandra, Manso Jose, Antonio, Pereira Pedro José, Barbosa, Davidović, Radoslav, Veljkovic, Nevena, Hajdu-Soltész, Borbála, Pajkos, Mátyás, Szaniszló, Tamás, Guharoy, Mainak, Lazar, Tamas, Macossay-Castillo, Mauricio, Tompa, Peter, Tosatto Silvio C., E., Caid, Predictors, DisProt, Curators, Università degli Studi di Padova = University of Padua (Unipd), Institut de minéralogie, de physique des matériaux et de cosmochimie (IMPMC), Muséum national d'Histoire naturelle (MNHN)-Institut de recherche pour le développement [IRD] : UR206-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Necci, Marco [0000-0001-9377-482X], Piovesan, Damiano [0000-0001-8210-2390], Tosatto, Silvio C. E. [0000-0003-4525-7793], Apollo - University of Cambridge Repository, Informatics and Applied Informatics, Chemistry, Basic (bio-) Medical Sciences, Department of Bio-engineering Sciences, Faculty of Sciences and Bioengineering Sciences, Structural Biology Brussels, Tosatto, Silvio CE [0000-0003-4525-7793], ANR-17-CE12-0016,FUNBRCA2,Caractérisation d'un nouveau site de liaison à l'ADN dans la protéine BRCA2(2017), Universita degli Studi di Padova, CAID Predictors, and DisProt Curators

Subjects
Protein Folding, Protein Conformation, Computer science, 631/45/612, analysis, [SDV]Life Sciences [q-bio], purl.org/becyt/ford/1.7 [https], MESH: Amino Acid Sequence, Biochemistry, purl.org/becyt/ford/1 [https], Protein structure, MESH: Protein Conformation, 631/114/2398, Databases, Protein, Biological sciences, ComputingMilieux_MISCELLANEOUS, MESH: Intrinsically Disordered Proteins, 0303 health sciences, 030302 biochemistry & molecular biology, disorder, Critical assessment, Protein folding, Protein Binding, Biotechnology, MESH: Computational Biology, MESH: Databases, Protein, disorder prediction, MESH: Protein Folding, Computational biology, Intrinsically disordered proteins, Orders of magnitude (entropy), 03 medical and health sciences, MESH: Software, Computational platforms and environments, 631/114/2411, Machine learning, Molecule, MESH: Protein Binding, [INFO]Computer Science [cs], Amino Acid Sequence, Molecular Biology, 030304 developmental biology, business.industry, Deep learning, Computational Biology, Proteins, Cell Biology, 631/114/1305, Intrinsically Disordered Proteins, CAID, 631/114/794, Protein structure predictions, Artificial intelligence, business, Software
Abstract

Intrinsically disordered proteins, defying the traditional protein structure–function paradigm, are a challenge to study experimentally. Because a large part of our knowledge rests on computational predictions, it is crucial that their accuracy is high. The Critical Assessment of protein Intrinsic Disorder prediction (CAID) experiment was established as a community-based blind test to determine the state of the art in prediction of intrinsically disordered regions and the subset of residues involved in binding. A total of 43 methods were evaluated on a dataset of 646 proteins from DisProt. The best methods use deep learning techniques and notably outperform physicochemical methods. The top disorder predictor has Fmax = 0.483 on the full dataset and Fmax = 0.792 following filtering out of bona fide structured regions. Disordered binding regions remain hard to predict, with Fmax = 0.231. Interestingly, computing times among methods can vary by up to four orders of magnitude., Results are presented from the first Critical Assessment of protein Intrinsic Disorder prediction (CAID) experiment, a community-based blind test to determine the state of the art in predicting intrinsically disordered regions in proteins.

Published
2021
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34. MobiDB: Intrinsically disordered proteins in 2021

Author

Piovesan, Damiano, Necci, Marco, Escobedo, Nahuel, Monzon, Alexander Miguel, Hatos, András, Mičetić, Ivan, Quaglia, Federica, Paladin, Lisanna, Ramasamy, Pathmanaban, Dosztányi, Zsuzsanna, Vranken, Wim, Davey, Norman N.E., Parisi, Gustavo, Fuxreiter, Mónika, Tosatto, Silvio S.C.E., Piovesan, Damiano, Necci, Marco, Escobedo, Nahuel, Monzon, Alexander Miguel, Hatos, András, Mičetić, Ivan, Quaglia, Federica, Paladin, Lisanna, Ramasamy, Pathmanaban, Dosztányi, Zsuzsanna, Vranken, Wim, Davey, Norman N.E., Parisi, Gustavo, Fuxreiter, Mónika, and Tosatto, Silvio S.C.E.

Abstract

The MobiDB database (URL: https://mobidb.org/) provides predictions and annotations for intrinsically disordered proteins. Here, we report recent developments implemented in MobiDB version 4, regarding the database format, with novel types of annotations and an improved update process. The new website includes a re-designed user interface, a more effective search engine and advanced API for programmatic access. The new database schema gives more flexibility for the users, as well as simplifying the maintenance and updates. In addition, the new entry page provides more visualisation tools including customizable feature viewer and graphs of the residue contact maps. MobiDB v4 annotates the binding modes of disordered proteins, whether they undergo disorder-to-order transitions or remain disordered in the bound state. In addition, disordered regions undergoing liquid-liquid phase separation or post-translational modifications are defined. The integrated information is presented in a simplified interface, which enables faster searches and allows large customized datasets to be downloaded in TSV, Fasta or JSON formats. An alternative advanced interface allows users to drill deeper into features of interest. A new statistics page provides information at database and proteome levels. The new MobiDB version presents state-of-the-art knowledge on disordered proteins and improves data accessibility for both computational and experimental users., SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2021

38. Intrinsically disordered protein mutations can drive cancer and their targeted interference extends therapeutic options

Author

Mészáros, Bálint, Hajdu-Soltész, Borbála, Zeke, András, and Dosztányi, Zsuzsanna

Abstract

Intrinsically disordered regions (IDRs) are important functional modules of several proteins, providing extra layers of regulation as switchable structural elements. Protein disorder has been associated with cancer, but it is unknown whether IDR mutations represent a distinct class of driver events associated with specific molecular mechanisms and system level properties, which would require dedicated targeting strategies. Based on an integrative computational approach, we identified 47 IDRs whose genetic mutations can be directly linked to cancer development. While not as common as alterations of globular domains, IDR mutations contribute to the emergence of the same cancer hallmarks through the modulation of distinct molecular mechanisms, increased interaction potential and specific functional repertoire. We demonstrate that in specific cancer subtypes, IDR mutations represent the key events driving tumorigenesis. However, treatment options for such patients are currently severely limited. We suggest targeting strategies that could enable successful therapeutic intervention for this subclass of cancer drivers, extending our options for personalized therapies.

Published
2020
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39. DisProt: intrinsic protein disorder annotation in 2020

Author

Hatos, András, Hajdu-Soltész, Borbála, Monzon, Alexander M., Palopoli, Nicolas, Álvarez, Lucía, Aykac-Fas, Burcu, Bassot, Claudio, Benítez, Guillermo I., Bevilacqua, Martina, Chasapi, Anastasia, Chemes, Lucia, Davey, Norman E., Davidović, Radoslav, Dunker, A. Keith, Elofsson, Arne, Gobeill, Julien, Foutel, Nicolás S. González, Sudha, Govindarajan, Guharoy, Mainak, Horvath, Tamas, Iglesias, Valentin, Kajava, Andrey V., Kovacs, Orsolya P., Lamb, John, Lambrughi, Matteo, Lazar, Tamas, Leclercq, Jeremy Y., Leonardi, Emanuela, Macedo-Ribeiro, Sandra, Macossay-Castillo, Mauricio, Maiani, Emiliano, Manso, José A., Marino-Buslje, Cristina, Martínez-Pérez, Elizabeth, Mészáros, Bálint, Mičetić, Ivan, Minervini, Giovanni, Murvai, Nikoletta, Necci, Marco, Ouzounis, Christos A., Pajkos, Mátyás, Paladin, Lisanna, Pancsa, Rita, Papaleo, Elena, Parisi, Gustavo, Pasche, Emilie, Barbosa Pereira, Pedro J., Promponas, Vasilis J., Pujols, Jordi, Quaglia, Federica, Ruch, Patrick, Salvatore, Marco, Schad, Eva, Szabo, Beata, Szaniszló, Tamás, Tamana, Stella, Tantos, Agnes, Veljkovic, Nevena, Ventura, Salvador, Vranken, Wim, Dosztányi, Zsuzsanna, Tompa, Peter, Tosatto, Silvio C. E., Piovesan, Damiano, Promponas, Vasilis J. [0000-0003-3352-4831], Universita degli Studi di Padova, Vinča Institute of Nuclear Sciences, University of Belgrade [Belgrade], Stockholm University, Laboratoire Leibniz (Leibniz - IMAG), Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique de Grenoble (INPG)-Université Joseph Fourier - Grenoble 1 (UJF), Laboratoire de biochimie théorique [Paris] (LBT (UPR_9080)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Institut de biologie physico-chimique (IBPC (FR_550)), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Reproductive Neuroscience Unit, Department of Obstetrics and Gynecology and Department of Neurobiology, Yale University School of Medicine, Centre de recherche en Biologie Cellulaire (CRBM), Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Modena e Reggio Emilia (UNIMORE), Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Instituto de Biologia Molecular e Celular (IBMC), Hungarian Academy of Sciences (MTA), Institute of Agrobiotechnology, National Center for Research and Technology, Universidad Nacional de Quilmes (UNQ), Université de Genève et Hôpitaux Universitaires de Genève (SIM), Hôpitaux Universitaires de Genève (HUG), Biophysics and Bioinformatics Laboratory, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona (UAB), Service d'informatique médicale (SIM), Hôpitaux de Genève, Department of Structural Biology, Biophysics Research Group [Budapest] (ELTE-MTA 'Lendület'), Department of Bio-engineering Sciences, Structural Biology Brussels, Faculty of Sciences and Bioengineering Sciences, Informatics and Applied Informatics, Chemistry, Basic (bio-) Medical Sciences, Instituto de Investigação e Inovação em Saúde, Université Joseph Fourier - Grenoble 1 (UJF)-Institut National Polytechnique de Grenoble (INPG)-Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot - Paris 7 (UPD7)-Institut de biologie physico-chimique (IBPC), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), Vrije Universiteit [Brussels] (VUB), Universitat Autònoma de Barcelona [Barcelona] (UAB), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Institut de biologie physico-chimique (IBPC (FR_550)), and Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Disordered proteins, Interface (Java), Disorder Ontology, [SDV]Life Sciences [q-bio], Interoperability, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Ontology (information science), Biology, 03 medical and health sciences, Annotation, Genetics, Database Issue, Databases, Protein, ComputingMilieux_MISCELLANEOUS, Data Curation, 030304 developmental biology, Graphical user interface, Structure (mathematical logic), 0303 health sciences, Intrinsically Disordered Proteins / chemistry, Information retrieval, Intrinsically disordered proteins, Data curation, Molecular sequence annotation, business.industry, 030302 biochemistry & molecular biology, Intrinsic protein, Biological Ontologies, Molecular Sequence Annotation, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Intrinsically Disordered Proteins, Dark proteome, Ontology, Intrisic protein disorder, Literature curation, business, Biological ontologies
Abstract

The Database of Protein Disorder (DisProt, URL: https://disprot.org) provides manually curated annotations of intrinsically disordered proteins from the literature. Here we report recent developments with DisProt (version 8), including the doubling of protein entries, a new disorder ontology, improvements of the annotation format and a completely new website. The website includes a redesigned graphical interface, a better search engine, a clearer API for programmatic access and a new annotation interface that integrates text mining technologies. The new entry format provides a greater flexibility, simplifies maintenance and allows the capture of more information from the literature. The new disorder ontology has been formalized and made interoperable by adopting the OWL format, as well as its structure and term definitions have been improved. The new annotation interface has made the curation process faster and more effective. We recently showed that new DisProt annotations can be effectively used to train and validate disorder predictors. We believe the growth of DisProt will accelerate, contributing to the improvement of function and disorder predictors and therefore to illuminate the 'dark' proteome. Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT) of Argentina [PICT-2015/3367, PICT-2017/1924]; Ministry of Education, Science and Technological Development of the Republic of Serbia [ON173001]; Vetenskapsrådet [2016-03798]; Hungarian National Research, Development, and Innovation Office (NKFIH) [FK-128133]; Italian Ministry of Health Young Investigator Grant [GR-2011-02347754]; Ministerio de Economía y Competitividad (MINECO) [BIO2016-78310-R]; ICREA (ICREA-Academia 2015); Fundac¸ão para a Ciência e a Tecnologia (FCT, Portugal); European Regional Development Fund [POCI-01-0145-FEDER-031173, POCI-01-0145-FEDER-029221]; Mexican National Council of Science and Technology (CONACYT) [215503]; Elixir-GR, Action ‘Reinforcement of the Research and Innovation Infrastructure’, Operational Programme ‘Competitiveness, Entrepreneurship and Innovation’ [NSRF 2014-2020]. co-financed by Greece and the European Union (European Regional Development Fund); Hungarian Academy of Sciences [PREMIUM-2017-48]; Carlsberg Distinguished Fellowship [CF18-0314]; Danmarks Grundforskningsfond [DNRF125]; National Research, Development and Innovation Office [K-125340]; Research Foundation Flanders (FWO) [G.0328.16N]; Hungarian Academy of Sciences [LP2014-18]; OTKA [K108798 and K124670]. This project has received funding from the European Union’s Horizon 2020 research and innovation programme [778247]. Funding for open access charge: European Union’s Horizon 2020 research and innovation programme [778247]. Conflict of interest statement. None declared.

Published
2020
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40. DisProt:Intrinsic protein disorder annotation in 2020

Author

Hatos, András, Hajdu-Soltész, Borbála, Monzon, Alexander M., Palopoli, Nicolas, Álvarez, Lucía, Aykac-Fas, Burcu, Bassot, Claudio, Benítez, Guillermo I., Bevilacqua, Martina, Chasapi, Anastasia, Chemes, Lucia, Davey, Norman E., Davidović, Radoslav, Dunker, A. Keith, Elofsson, Arne, Gobeill, Julien, Foutel, Nicolás S.González, Sudha, Govindarajan, Guharoy, Mainak, Horvath, Tamas, Iglesias, Valentin, Kajava, Andrey V., Kovacs, Orsolya P., Lamb, John, Lambrughi, Matteo, Lazar, Tamas, Leclercq, Jeremy Y., Leonardi, Emanuela, MacEdo-Ribeiro, Sandra, MacOssay-Castillo, Mauricio, Maiani, Emiliano, Manso, José A., Marino-Buslje, Cristina, Martínez-Pérez, Elizabeth, Mészáros, Bálint, Mičetić, Ivan, Minervini, Giovanni, Murvai, Nikoletta, Necci, Marco, Ouzounis, Christos A., Pajkos, Mátyás, Paladin, Lisanna, Pancsa, Rita, Papaleo, Elena, Parisi, Gustavo, Pasche, Emilie, Barbosa Pereira, Pedro J., Promponas, Vasilis J., Pujols, Jordi, Quaglia, Federica, Ruch, Patrick, Salvatore, Marco, Schad, Eva, Szabo, Beata, Szaniszló, Tamás, Tamana, Stella, Tantos, Agnes, Veljkovic, Nevena, Ventura, Salvador, Vranken, Wim, Dosztányi, Zsuzsanna, Tompa, Peter, Tosatto, Silvio C.E., Piovesan, Damiano, Hatos, András, Hajdu-Soltész, Borbála, Monzon, Alexander M., Palopoli, Nicolas, Álvarez, Lucía, Aykac-Fas, Burcu, Bassot, Claudio, Benítez, Guillermo I., Bevilacqua, Martina, Chasapi, Anastasia, Chemes, Lucia, Davey, Norman E., Davidović, Radoslav, Dunker, A. Keith, Elofsson, Arne, Gobeill, Julien, Foutel, Nicolás S.González, Sudha, Govindarajan, Guharoy, Mainak, Horvath, Tamas, Iglesias, Valentin, Kajava, Andrey V., Kovacs, Orsolya P., Lamb, John, Lambrughi, Matteo, Lazar, Tamas, Leclercq, Jeremy Y., Leonardi, Emanuela, MacEdo-Ribeiro, Sandra, MacOssay-Castillo, Mauricio, Maiani, Emiliano, Manso, José A., Marino-Buslje, Cristina, Martínez-Pérez, Elizabeth, Mészáros, Bálint, Mičetić, Ivan, Minervini, Giovanni, Murvai, Nikoletta, Necci, Marco, Ouzounis, Christos A., Pajkos, Mátyás, Paladin, Lisanna, Pancsa, Rita, Papaleo, Elena, Parisi, Gustavo, Pasche, Emilie, Barbosa Pereira, Pedro J., Promponas, Vasilis J., Pujols, Jordi, Quaglia, Federica, Ruch, Patrick, Salvatore, Marco, Schad, Eva, Szabo, Beata, Szaniszló, Tamás, Tamana, Stella, Tantos, Agnes, Veljkovic, Nevena, Ventura, Salvador, Vranken, Wim, Dosztányi, Zsuzsanna, Tompa, Peter, Tosatto, Silvio C.E., and Piovesan, Damiano

Abstract

The Database of Protein Disorder (DisProt, URL: https://disprot.org) provides manually curated annotations of intrinsically disordered proteins from the literature. Here we report recent developments with DisProt (version 8), including the doubling of protein entries, a new disorder ontology, improvements of the annotation format and a completely new website. The website includes a redesigned graphical interface, a better search engine, a clearer API for programmatic access and a new annotation interface that integrates text mining technologies. The new entry format provides a greater flexibility, simplifies maintenance and allows the capture of more information from the literature. The new disorder ontology has been formalized and made interoperable by adopting the OWL format, as well as its structure and term definitions have been improved. The new annotation interface has made the curation process faster and more effective. We recently showed that new DisProt annotations can be effectively used to train and validate disorder predictors. We believe the growth of DisProt will accelerate, contributing to the improvement of function and disorder predictors and therefore to illuminate the 'dark' proteome.

Published
2020

47. MobiDB: intrinsically disordered proteins in 2021

Author

Piovesan, Damiano, primary, Necci, Marco, additional, Escobedo, Nahuel, additional, Monzon, Alexander Miguel, additional, Hatos, András, additional, Mičetić, Ivan, additional, Quaglia, Federica, additional, Paladin, Lisanna, additional, Ramasamy, Pathmanaban, additional, Dosztányi, Zsuzsanna, additional, Vranken, Wim F, additional, Davey, Norman E, additional, Parisi, Gustavo, additional, Fuxreiter, Monika, additional, and Tosatto, Silvio C E, additional

Published
2020
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