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1. A STRP-ed definition of Structured Tandem Repeats in Proteins

Author

Monzon, Alexander Miguel, Arrías, Paula Nazarena, Elofsson, Arne, Mier, Pablo, Andrade-Navarro, Miguel A., Bevilacqua, Martina, Clementel, Damiano, Bateman, Alex, Hirsh, Layla, Fornasari, Maria Silvina, Parisi, Gustavo, Piovesan, Damiano, Kajava, Andrey V., and Tosatto, Silvio C.E.

Published
2023
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2. A STRP-ed definition of Structured Tandem Repeats in Proteins

Author

Miguel Monzon, Alexander, primary, Arrías, Paula N., additional, Elofsson, Arne, additional, Mier, Pablo, additional, Andrade-Navarro, Miguel A., additional, Bevilacqua, Martina, additional, Clementel, Damiano, additional, Bateman, Alex, additional, Hirsh, Layla, additional, Silvina Fornasari, Maria, additional, Parisi, Gustavo, additional, Piovesan, Damiano, additional, Kajava, Andrey V., additional, and Tosatto, Silvio C.E., additional

Published
2023
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3. MobiDB: 10 years of intrinsically disordered proteins

Author

Piovesan, Damiano, primary, Del Conte, Alessio, additional, Clementel, Damiano, additional, Monzon, Alexander Miguel, additional, Bevilacqua, Martina, additional, Aspromonte, Maria Cristina, additional, Iserte, Javier A, additional, Orti, Fernando E, additional, Marino-Buslje, Cristina, additional, and Tosatto, Silvio C E, additional

Published
2022
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6. 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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7. 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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8. 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

9. RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures

Author

Paladin, Lisanna, primary, Bevilacqua, Martina, additional, Errigo, Sara, additional, Piovesan, Damiano, additional, Mičetić, Ivan, additional, Necci, Marco, additional, Monzon, Alexander Miguel, additional, Fabre, Maria Laura, additional, Lopez, Jose Luis, additional, Nilsson, Juliet F, additional, Rios, Javier, additional, Menna, Pablo Lorenzano, additional, Cabrera, Maia, additional, Buitron, Martin Gonzalez, additional, Kulik, Mariane Gonçalves, additional, Fernandez-Alberti, Sebastian, additional, Fornasari, Maria Silvina, additional, Parisi, Gustavo, additional, Lagares, Antonio, additional, Hirsh, Layla, additional, Andrade-Navarro, Miguel A, additional, Kajava, Andrey V, additional, and Tosatto, Silvio C E, additional

Published
2020
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11. 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 S., 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, Veljković, Nevena V., 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 S., 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, Veljković, Nevena V., 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
2019

12. DisProt: intrinsic protein disorder annotation in 2020

Author

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

Published
2019
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13. RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures.

Author

Paladin, Lisanna, Bevilacqua, Martina, Errigo, Sara, Piovesan, Damiano, Mičetić, Ivan, Necci, Marco, Monzon, Alexander Miguel, Fabre, Maria Laura, Lopez, Jose Luis, Nilsson, Juliet F, Rios, Javier, Menna, Pablo Lorenzano, Cabrera, Maia, Buitron, Martin Gonzalez, Kulik, Mariane Gonçalves, Fernandez-Alberti, Sebastian, Fornasari, Maria Silvina, Parisi, Gustavo, Lagares, Antonio, and Hirsh, Layla

Published
2021
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14. ProSeqViewer: an interactive, responsive and efficient TypeScript library for visualization of sequences and alignments in web applications.

Author

Bevilacqua, Martina, Paladin, Lisanna, Tosatto, Silvio C E, and Piovesan, Damiano

Subjects
*SEQUENCE alignment, *WEB-based user interfaces, *AMINO acid sequence, *VISUALIZATION, *BIOLOGICAL databases, *LIBRARY websites
Abstract

Summary 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. Availability and implementation ProSeqViewer is an open-source TypeScript library compatible with state-of-the-art website environments. The source code and an extensive documentation including use cases are available from the URL: https://github.com/BioComputingUP/ProSeqViewer. [ABSTRACT FROM AUTHOR]

Published
2022
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16. DisProt: intrinsic protein disorder annotation in 2020.

Author

Hatos A, Hajdu-Soltész B, Monzon AM, Palopoli N, Álvarez L, Aykac-Fas B, Bassot C, Benítez GI, Bevilacqua M, Chasapi A, Chemes L, Davey NE, Davidović R, Dunker AK, Elofsson A, Gobeill J, Foutel NSG, Sudha G, Guharoy M, Horvath T, Iglesias V, Kajava AV, Kovacs OP, Lamb J, Lambrughi M, Lazar T, Leclercq JY, Leonardi E, Macedo-Ribeiro S, Macossay-Castillo M, Maiani E, Manso JA, Marino-Buslje C, Martínez-Pérez E, Mészáros B, Mičetić I, Minervini G, Murvai N, Necci M, Ouzounis CA, Pajkos M, Paladin L, Pancsa R, Papaleo E, Parisi G, Pasche E, Barbosa Pereira PJ, Promponas VJ, Pujols J, Quaglia F, Ruch P, Salvatore M, Schad E, Szabo B, Szaniszló T, Tamana S, Tantos A, Veljkovic N, Ventura S, Vranken W, Dosztányi Z, Tompa P, Tosatto SCE, and Piovesan D

Subjects
Biological Ontologies, Data Curation, Molecular Sequence Annotation, Databases, Protein, Intrinsically Disordered Proteins chemistry
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., (© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2020
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