Critical assessment of protein intrinsic disorder prediction
Necci, Marco (University of Padua. Department of Biomedical Sciences)
Piovesan, Damiano (University of Padua. Department of Biomedical Sciences)
Hoque, M. T. (University of New Orleans. Computer Science)
Walsh, Ian (Agency for Science, Technology and Research. Bioprocessing Technology Institute)
Iqbal, Sumaiya (Broad Institute of MIT and Harvard. Center for Psychiatric Research)
Vendruscolo, Michele (University of Cambridge. Centre for Misfolding Diseases. Department of Chemistry)
Sormanni, Pietro (University of Cambridge. Centre for Misfolding Diseases. Department of Chemistry)
Wang, Chen (Columbia University. Department of Medicine)
Raimondi, Daniele (ESAT-STADIUS. KU Leuven)
Sharma, Ronesh (Fiji National University)
Zhou, Yaoqi (Griffith University. Institute for Glycomics and School of Information and Communication Technology)
Litfin, Thomas (Griffith University. Institute for Glycomics and School of Information and Communication Technology)
Galzitskaya, Oxxana Valerianovna (Russian Academy of Sciences. Institute of Theoretical and Experimental Biophysics)
Lobanov, Michail Yu (Russian Academy of Sciences. Institute of Protein Research)
Vranken, Wim (Vrije Universiteit Brussel. Interuniversity Institute of Bioinformatics in Brussels)
Wallner, Björn (Linköping University. Department of Physics, Chemistry and Biology)
Mirabello, Claudio (Linköping University. Department of Physics, Chemistry and Biology)
Malhis, Nawar (University of British Columbia. Michael Smith Laboratories)
Dosztányi, Zsuzsanna (Eötvös Loránd University. Department of Biochemistry)
Erdős, Gábor (Eötvös Loránd University. Department of Biochemistry)
Mészáros, Bálint (European Molecular Biology Laboratory. Structural and Computational Biology Unit)
Gao, Jianzhao (Nankai University. School of Mathematical Sciences and LPMC)
Wang, Kui (Nankai University. School of Mathematical Sciences and LPMC)
Hu, Gang (Nankai University. School of Statistics and Data Science)
Wu, Zhonghua (Nankai University. School of Mathematical Sciences and LPMC)
Sharma, Alok (University of the South Pacific. School of Engineering and Physics)
Hanson, Jack (Griffith University. School of Engineering and Built Environment. Signal Processing Laboratory Griffith University. School of Engineering and Built Environment. Signal Processing Laboratory Signal Processing Laboratory. School of Engineering and Built Environment. Griffith University)
Callebaut, Isabelle (Sorbonne Université. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie. Muséum National d'Histoire Naturelle)
Bitard-Feildel, Tristan (Sorbonne Université. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie. Muséum National d'Histoire Naturelle)
Orlando, Gabriele (VIB-KU Leuven. Switch Laboratorium.)
Peng, Zhenling (Tianjin University. Center for Applied Mathematics)
Xu, Jinbo (Toyota Technological Institute at Chicago)
Wang, Sheng (Toyota Technological Institute at Chicago)
Jones, David T. (University College London)
Cozzetto, Domenico (University College London)
Meng, Fanchi (University of Alberta. Department of Electrical and Computer Engineering)
Yan, Jing (University of Alberta. Department of Electrical and Computer Engineering)
Gsponer, Jörg (University of British Columbia. Michael Smith Laboratories)
Cheng, Jianlin (University of Missouri. Department of Electrical Engineering and Computer Science)
Wu, Tianqi (University of Missouri. Department of Electrical Engineering and Computer Science)
Kurgan, Lukasz (Virginia Commonwealth University. Department of Computer Science)
Promponas, Vasilis J. (University of Cyprus. Department of Biological Sciences. Bioinformatics Research Laboratory)
Tamana, Stella (University of Cyprus. Department of Biological Sciences. Bioinformatics Research Laboratory)
Marino-Buslje, Cristina (Fundación Instituto Leloir (Buenos Aires, Argentina))
Martínez-Pérez, Elisabeth (Fundación Instituto Leloir (Buenos Aires, Argentina))
Chasapi, Anastasia (Centre for Research & Technology Hellas. Chemical Process & Energy Resources Institute)
Ouzounis, Christos (Centre for Research & Technology Hellas. Chemical Process & Energy Resources Institute)
Dunker, A. Keith (Indiana University School of Medicine. Center for Computational Biology and Bioinformatics)
Kajava, Andrey V (University of Montpellier. Centre de Recherche en Biologie cellulaire de Montpellier)
Leclercq, Jeremy Y. (University of Montpellier. Centre de Recherche en Biologie cellulaire de Montpellier)
Aykac-Fas, Burcu (Danish Cancer Society Research Center)
Lambrughi, Matteo (Danish Cancer Society Research Center)
Maiani, Emiliano (Danish Cancer Society Research Center)
Papaleo, Elena (Danish Cancer Society Research Center)
Chemes, Lucía Beatriz (Universidad Nacional de San Martín. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Biotecnológicas)
Álvarez, Lucía (Universidad Nacional de San Martín. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Biotecnológicas)
González-Foutel, Nicolás S. (Universidad Nacional de San Martín. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Biotecnológicas)
Iglesias, Valentin (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)
Pujols Pujol, Jordi (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Ventura, Salvador (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Palopoli, Nicolas (Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología)
Benítez, Guillermo I (Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología)
Parisi, Gustavo (Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología)
Bassot, Claudio (Stockholm University. Department of Biochemistry and Biophysics and Science for Life Laboratory)
Elofsson, Arne (Stockholm University. Department of Biochemistry and Biophysics and Science for Life Laboratory)
Govindarajan, Sudha (Stockholm University. Department of Biochemistry and Biophysics and Science for Life Laboratory)
Lamb, John (Stockholm University. Department of Biochemistry and Biophysics and Science for Life Laboratory)
Salvatore, Marco (Copenhagen University. Department of Biology)
Hatos, András (Università di Padova. Dipartimento di Scienze Biomediche)
Monzon, Alexander Miguel (Università di Padova. Dipartimento di Scienze Biomediche)
Bevilacqua, Martina (Università di Padova. Dipartimento di Scienze Biomediche)
Mičetić, Ivan (Università di Padova. Dipartimento di Scienze Biomediche)
Minervini, Giovanni (Università di Padova. Dipartimento di Scienze Biomediche)
Paladin, Lisanna (Università di Padova. Dipartimento di Scienze Biomediche)
Quaglia, Federica (Università di Padova. Dipartimento di Scienze Biomediche)
Leonardi, Emanuela (Università di Padova)
Davey, Norman E. (The Institute of Cancer Research. Chelsea)
Horvath, Tamas (Research Centre for Natural Sciences. Institute of Enzymology)
Kovacs, Orsolya Panna (Research Centre for Natural Sciences. Institute of Enzymology)
Murvai, Nikoletta (Research Centre for Natural Sciences. Institute of Enzymology)
Pancsa, Rita (Research Centre for Natural Sciences. Institute of Enzymology)
Schad, Eva (Research Centre for Natural Sciences. Institute of Enzymology)
Szabo, Beata (Research Centre for Natural Sciences. Institute of Enzymology)
Tantos, Agnes (Research Centre for Natural Sciences. Institute of Enzymology)
Macedo-Ribeiro, Sandra (Universidade do Porto. Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde)
Manso, Jose Antonio (Universidade do Porto. Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde)
Barbosa Pereira, Pedro José (Universidade do Porto. Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde)
Davidović, Radoslav (University of Belgrade. Vinča Institute of Nuclear Sciences - National Institute of thе Republic of Serbia.)
Veljkovic, Nevena (University of Belgrade. Vinča Institute of Nuclear Sciences - National Institute of thе Republic of Serbia.)
Hajdu-Soltész, Borbála (Eötvös Loránd University. Department of Biochemistry)
Pajkos, Mátyás (Eötvös Loránd University. Department of Biochemistry)
Szaniszló, Tamás (Eötvös Loránd University. Department of Biochemistry)
Guharoy, Mainak (Vrije Universiteit Brussel. Structural Biology Brussels)
Lazar, Tamas (Vrije Universiteit Brussel. Structural Biology Brussels)
Macossay-Castillo, Mauricio (Vrije Universiteit Brussel. Structural Biology Brussels)
Tompa, Peter (Vrije Universiteit Brussel. Structural Biology Brussels)
Tosatto, Silvio (University of Padua. Department of Biomedical Sciences)

Data:	2021
Resum:	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.
Ajuts:	European Commission 778247
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Llengua:	Anglès
Document:	Article ; recerca ; Versió publicada
Matèria:	Amino Acid Sequence ; Computational Biology ; Databases, Protein ; Intrinsically Disordered Proteins ; Protein Binding ; Protein Conformation ; Protein Folding ; Software
Publicat a:	Nature Methods, Vol. 18 (May 2021) , p. 472-481, ISSN 1548-7105

DOI: 10.1038/s41592-021-01117-3
PMID: 33875885

14 p, 2.8 MB

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