Critical assessment of protein intrinsic disorder prediction - Sorbonne Université
Journal Articles Nature Methods Year : 2021

Critical assessment of protein intrinsic disorder prediction

Marco Necci (1) , Damiano Piovesan (1) , Silvio C E Tosatto (1) , Md Tamjidul Hoque , Ian Walsh , Sumaiya Iqbal , Michele Vendruscolo , Pietro Sormanni , Chen Wang , Daniele Raimondi , Ronesh Sharma , Yaoqi Zhou , Thomas Litfin , Oxana Valerianovna Galzitskaya , Michail Yu. Lobanov , Wim Vranken , Björn Wallner , Claudio Mirabello , Nawar Malhis , Zsuzsanna Dosztányi , Gábor Erdős , Bálint Mészáros , Jianzhao Gao , Kui Wang , Gang Hu , Zhonghua Wu , Alok Sharma , Jack Hanson , Kuldip Paliwal , Isabelle Callebaut (2) , Tristan Bitard-Feildel , Gabriele Orlando , Zhenling Peng , Jinbo Xu , Sheng Wang , David T. Jones , Domenico Cozzetto , Fanchi Meng , Jing Yan , Jörg Gsponer , Jianlin Cheng , Tianqi Wu , Lukasz Kurgan , Vasilis J. Promponas , Stella Tamana , Cristina Marino-Buslje , Elizabeth Martínez-Pérez , Anastasia Chasapi , Christos Ouzounis , A. Keith Dunker , Andrey V. Kajava , Jeremy Y. Leclercq , Burcu Aykac-Fas , Matteo Lambrughi , Emiliano Maiani , Elena Papaleo , Lucia Beatriz Chemes , Lucía Álvarez , Nicolás S. González-Foutel , Valentin Iglesias , Jordi Pujols , Salvador Ventura , Nicolás Palopoli , Guillermo Ignacio Benítez , Gustavo Parisi , Claudio Bassot , Arne Elofsson , Sudha Govindarajan , John Lamb , Marco Salvatore , András Hatos , Alexander Miguel Monzon , Martina Bevilacqua , Ivan Mičetić , Giovanni Minervini , Lisanna Paladin , Federica Quaglia , Emanuela Leonardi , Norman Davey , Tamas Horvath , Orsolya Panna Kovacs , Nikoletta Murvai , Rita Pancsa , Eva Schad , Beata Szabo , Agnes Tantos , Sandra Macedo-Ribeiro , Jose Antonio Manso , Pedro José Barbosa Pereira , Radoslav Davidović , Nevena Veljkovic , Borbála Hajdu-Soltész , Mátyás Pajkos , Tamás Szaniszló , Mainak Guharoy , Tamas Lazar , Mauricio Macossay-Castillo , Peter Tompa
Md Tamjidul Hoque
  • Function : Author
Ian Walsh
  • Function : Author
Sumaiya Iqbal
  • Function : Author
Michele Vendruscolo
  • Function : Author
Pietro Sormanni
  • Function : Author
Chen Wang
Daniele Raimondi
  • Function : Author
Ronesh Sharma
  • Function : Author
Yaoqi Zhou
  • Function : Author
Thomas Litfin
  • Function : Author
Oxana Valerianovna Galzitskaya
  • Function : Author
Michail Yu. Lobanov
  • Function : Author
Wim Vranken
Björn Wallner
  • Function : Author
Claudio Mirabello
  • Function : Author
Nawar Malhis
  • Function : Author
Zsuzsanna Dosztányi
Gábor Erdős
Bálint Mészáros
Jianzhao Gao
  • Function : Author
Kui Wang
  • Function : Author
Gang Hu
  • Function : Author
Zhonghua Wu
  • Function : Author
Alok Sharma
  • Function : Author
Jack Hanson
  • Function : Author
Kuldip Paliwal
  • Function : Author
Tristan Bitard-Feildel
  • Function : Author
Gabriele Orlando
  • Function : Author
Zhenling Peng
  • Function : Author
Jinbo Xu
  • Function : Author
Sheng Wang
  • Function : Author
David T. Jones
  • Function : Author
Domenico Cozzetto
  • Function : Author
Fanchi Meng
  • Function : Author
Jing Yan
  • Function : Author
Jörg Gsponer
  • Function : Author
Jianlin Cheng
  • Function : Author
Tianqi Wu
  • Function : Author
Lukasz Kurgan
  • Function : Author
Vasilis J. Promponas
  • Function : Author
Stella Tamana
  • Function : Author
Cristina Marino-Buslje
Elizabeth Martínez-Pérez
Anastasia Chasapi
Christos Ouzounis
  • Function : Author
A. Keith Dunker
  • Function : Author
Andrey V. Kajava
  • Function : Author
Jeremy Y. Leclercq
  • Function : Author
Burcu Aykac-Fas
Matteo Lambrughi
Emiliano Maiani
Elena Papaleo
Lucia Beatriz Chemes
  • Function : Author
Lucía Álvarez
  • Function : Author
Nicolás S. González-Foutel
  • Function : Author
Valentin Iglesias
  • Function : Author
Jordi Pujols
Salvador Ventura
Nicolás Palopoli
Guillermo Ignacio Benítez
  • Function : Author
Gustavo Parisi
Claudio Bassot
Arne Elofsson
Sudha Govindarajan
  • Function : Author
John Lamb
  • Function : Author
Marco Salvatore
  • Function : Author
András Hatos
Alexander Miguel Monzon
  • Function : Author
Martina Bevilacqua
  • Function : Author
Ivan Mičetić
  • Function : Author
Giovanni Minervini
Lisanna Paladin
  • Function : Author
Federica Quaglia
Emanuela Leonardi
Norman Davey
  • Function : Author
Tamas Horvath
  • Function : Author
Orsolya Panna Kovacs
  • Function : Author
Nikoletta Murvai
  • Function : Author
Rita Pancsa
Eva Schad
Beata Szabo
  • Function : Author
Agnes Tantos
  • Function : Author
Sandra Macedo-Ribeiro
Jose Antonio Manso
  • Function : Author
Pedro José Barbosa Pereira
  • Function : Author
Radoslav Davidović
Nevena Veljkovic
Borbála Hajdu-Soltész
  • Function : Author
Mátyás Pajkos
Tamás Szaniszló
Mainak Guharoy
  • Function : Author
Tamas Lazar
Mauricio Macossay-Castillo
  • Function : Author
Peter Tompa

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 F max = 0.483 on the full dataset and F max = 0.792 following filtering out of bona fide structured regions. Disordered binding regions remain hard to predict, with F max = 0.231. Interestingly, computing times among methods can vary by up to four orders of magnitude.
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Dates and versions

hal-03329755 , version 2 (11-10-2021)
hal-03329755 , version 1 (11-10-2021)

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Cite

Marco Necci, Damiano Piovesan, Silvio C E Tosatto, Md Tamjidul Hoque, Ian Walsh, et al.. Critical assessment of protein intrinsic disorder prediction. Nature Methods, 2021, 18 (5), pp.472 - 481. ⟨10.1038/s41592-021-01117-3⟩. ⟨hal-03329755v2⟩
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