Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment
Andriy Kryshtafovych
(1)
,
John Moult
(2)
,
Wendy M Billings
(3)
,
Dennis Della Corte
(3)
,
Krzysztof Fidelis
(1)
,
Sohee Kwon
(4)
,
Kliment Olechnovič
(5)
,
Chaok Seok
(4)
,
Česlovas Venclovas
(5)
,
Jonghun Won
(4)
,
Badri Adhikari
(6)
,
Recep Adiyaman
(7)
,
Joaquim Aguirre-Plans
(8)
,
Ivan Anishchenko
(9)
,
Minkyung Baek
(9)
,
David Baker
(9)
,
Frederico Baldassarre
(10)
,
Jacob Barger
(6)
,
Sutanu Bhattacharya
(11)
,
Debswapna Bhattacharya
(11)
,
Mor Bitton
(12)
,
Renzhi Cao
(13)
,
Jianlin Cheng
(14)
,
Charles Christoffer
(15)
,
Cezary Czaplewski
(16)
,
Arne Elofsson
(17)
,
Eshel Faraggi
(18)
,
Michael Feig
(19)
,
Narcis Fernandez-Fuentes
(20)
,
Nick Grishin
(21)
,
Sergei Grudinin
(22, 22)
,
Zhiye Guo
(14)
,
Yuya Hanazono
(23)
,
Demis Hassabis
(24)
,
Bryce Hedelius
(3)
,
Lim Heo
(19)
,
Naozumi Hiranuma
(25)
,
Cassandra Hunt
(13)
,
Ilia Igashov
(26)
,
Takashi Ishida
(27)
,
Robert L. Jernigan
(28)
,
David Jones
(29)
,
John Jumper
(24)
,
Maria Kadukova
(26)
,
Shaun Kandathil
(29)
,
Chen Keasar
(12)
,
Daisuke Kihara
(15)
,
Lisa Kinch
(21)
,
Yasuomi Kiyota
(30)
,
Andrzje Kloczkowski
(31)
,
Pushmeet Kohli
(24)
,
Mateusz Kogut
(16)
,
Elodie Laine
(32)
,
Cade Lilley
(13)
,
Jian Liu
(14)
,
Adam Liwo
(16)
,
Emilia Lubecka
(16)
,
Arup Mondal
(33)
,
Connor J. Morris
(3)
,
Liam Mcguffin
(7)
,
Alexis Molina
(34)
,
Tsukasa Nakamura
(35)
,
Baldo Oliva
(8)
,
Alberto Perez
(33)
,
Gabriele Pozzati
(17)
,
Daipayan Sarkar
(15)
,
Rin Sato
(27)
,
Torsten Schwede
(36)
,
Bikash Shrestha
(6)
,
Tomer Sidi
(12)
,
Gabriel Studer
(36)
,
Md Hossain Shuvo
(11)
,
Mayuko Takeda-Shitaka
(30)
,
Yuma Takei
(27)
,
Genki Terashi
(15)
,
Kentaro Tomii
(37)
,
Yuko Tsuchiya
(37)
,
Kathryn Tunyasuvunakool
(24)
,
Björn Waliner
(38)
,
Tianqi Wu
(14)
,
Jinbo Xu
(39)
,
Yu Yamamori
(37)
,
Chengxin Zhang
(40)
,
Yang Zhang
(40)
,
Wei Zheng
(40)
1
UC Davis -
University of California [Davis]
2 IBBR - Institute for Bioscience and Biotechnology Research [Rockville, MD, États-Unis]
3 BYU - Brigham Young University
4 SNU - Seoul National University [Seoul]
5 Vilnius University [Vilnius]
6 University of Missouri [St. Louis]
7 UOR - University of Reading
8 UPF - Universitat Pompeu Fabra [Barcelona]
9 University of Washington - Biorobotics Lab
10 KTH - KTH Royal Institute of Technology [Stockholm]
11 AU - Auburn University
12 BGU - Ben-Gurion University of the Negev
13 PLU - Pacific Lutheran University [Tacoma]
14 Mizzou - University of Missouri [Columbia]
15 Purdue University [West Lafayette]
16 UG - University of Gdańsk
17 Stockholm University
18 IUPUI - Indiana University - Purdue University Indianapolis
19 Michigan State University [East Lansing]
20 Aberystwyth University
21 University of Texas Southwestern Medical Center
22 DAO - Données, Apprentissage et Optimisation
23 QST - National Institutes for Quantum Science and Technology [Chiba]
24 DeepMind [London]
25 University of Washington [Seattle]
26 MIPT - Moscow Institute of Physics and Technology [Moscow]
27 TITECH - Tokyo Institute of Technology [Tokyo]
28 ISU - Iowa State University
29 UCL - University College London [UCL]
30 Kitasato University
31 OSU - The Ohio State University [Columbus]
32 CQSB - Biologie Computationnelle, Quantitative et Synthétique [Paris] (ex LCQB)
33 UF - University of Florida [Gainesville]
34 BSC-CNS - Barcelona Supercomputing Center - Centro Nacional de Supercomputacion
35 Tohoku University [Sendai]
36 Unibas - Université de Bâle = University of Basel = Basel Universität
37 AIST - National Institute of Advanced Industrial Science and Technology
38 LIU - Linköping University
39 TTIC - Toyota Technological Institute at Chicago [Chicago]
40 UMich - Université du Michigan = University of Michigan [Ann Arbor]
2 IBBR - Institute for Bioscience and Biotechnology Research [Rockville, MD, États-Unis]
3 BYU - Brigham Young University
4 SNU - Seoul National University [Seoul]
5 Vilnius University [Vilnius]
6 University of Missouri [St. Louis]
7 UOR - University of Reading
8 UPF - Universitat Pompeu Fabra [Barcelona]
9 University of Washington - Biorobotics Lab
10 KTH - KTH Royal Institute of Technology [Stockholm]
11 AU - Auburn University
12 BGU - Ben-Gurion University of the Negev
13 PLU - Pacific Lutheran University [Tacoma]
14 Mizzou - University of Missouri [Columbia]
15 Purdue University [West Lafayette]
16 UG - University of Gdańsk
17 Stockholm University
18 IUPUI - Indiana University - Purdue University Indianapolis
19 Michigan State University [East Lansing]
20 Aberystwyth University
21 University of Texas Southwestern Medical Center
22 DAO - Données, Apprentissage et Optimisation
23 QST - National Institutes for Quantum Science and Technology [Chiba]
24 DeepMind [London]
25 University of Washington [Seattle]
26 MIPT - Moscow Institute of Physics and Technology [Moscow]
27 TITECH - Tokyo Institute of Technology [Tokyo]
28 ISU - Iowa State University
29 UCL - University College London [UCL]
30 Kitasato University
31 OSU - The Ohio State University [Columbus]
32 CQSB - Biologie Computationnelle, Quantitative et Synthétique [Paris] (ex LCQB)
33 UF - University of Florida [Gainesville]
34 BSC-CNS - Barcelona Supercomputing Center - Centro Nacional de Supercomputacion
35 Tohoku University [Sendai]
36 Unibas - Université de Bâle = University of Basel = Basel Universität
37 AIST - National Institute of Advanced Industrial Science and Technology
38 LIU - Linköping University
39 TTIC - Toyota Technological Institute at Chicago [Chicago]
40 UMich - Université du Michigan = University of Michigan [Ann Arbor]
Andriy Kryshtafovych
- Fonction : Auteur
- PersonId : 775022
- ORCID : 0000-0001-5066-7178
John Moult
- Fonction : Auteur
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Dennis Della Corte
- Fonction : Auteur
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Krzysztof Fidelis
- Fonction : Auteur
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- ORCID : 0000-0002-8061-412X
Chaok Seok
- Fonction : Auteur
- PersonId : 765067
- ORCID : 0000-0002-1419-9888
Frederico Baldassarre
- Fonction : Auteur
- PersonId : 1118716
Charles Christoffer
- Fonction : Auteur
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- ORCID : 0000-0002-6163-6323
Cezary Czaplewski
- Fonction : Auteur
- PersonId : 767440
- ORCID : 0000-0002-0294-3403
Arne Elofsson
- Fonction : Auteur
- PersonId : 792611
- ORCID : 0000-0002-7115-9751
- IdRef : 242123236
Sergei Grudinin
- Fonction : Auteur
- PersonId : 175316
- IdHAL : sergei-grudinin
- ORCID : 0000-0002-1903-7220
- IdRef : 186189729
Takashi Ishida
- Fonction : Auteur
- PersonId : 765069
- ORCID : 0000-0001-5167-9971
Daisuke Kihara
- Fonction : Auteur
- PersonId : 765070
- ORCID : 0000-0003-4091-6614
- IdRef : 155148435
Elodie Laine
- Fonction : Auteur
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- IdHAL : elodie-laine
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- IdRef : 143454927
Gabriele Pozzati
- Fonction : Auteur
- PersonId : 817399
- ORCID : 0000-0002-4303-9939
Torsten Schwede
- Fonction : Auteur
- PersonId : 775024
- ORCID : 0000-0003-2715-335X
- IdRef : 128202866
Yang Zhang
- Fonction : Auteur
- PersonId : 757354
- ORCID : 0000-0003-4102-2671
Wei Zheng
- Fonction : Auteur
- PersonId : 756070
- ORCID : 0000-0003-1226-070X
Résumé
Critical Assessment of Structure Prediction (CASP) is an organization aimed at advancing the state of the art in computing protein structure from sequence. In the spring of 2020, CASP launched a community project to compute the structures of the most structurally challenging proteins coded for in the SARS-CoV-2 genome. Forty-seven research groups submitted over 3000 three-dimensional models and 700 sets of accuracy estimates on 10 proteins. The resulting models were released to the public. CASP community members also worked together to provide estimates of local and global accuracy and identify structure-based domain boundaries for some proteins. Subsequently, two of these structures (ORF3a and ORF8) have been solved experimentally, allowing assessment of both model quality and the accuracy estimates. Models from the AlphaFold2 group were found to have good agreement with the experimental structures, with main chain GDT_TS accuracy scores ranging from 63 (a correct topology) to 87 (competitive with experiment).
Domaines
| Origine | Fichiers produits par l'(les) auteur(s) |
|---|---|
| licence |
