Modeling SARS-CoV-2 proteins in the CASP-commons experiment

Kryshtafovych, Andriy; Moult, John; Billings, Wendy M.; Della Corte, Dennis; Fidelis, Krzysztof; Kwon, Sohee; Olechnovič, Kliment; Seok, Chaok; Venclovas, Česlovas; Won, Jonghun

doi:10.1002/prot.26231

Modeling SARS-CoV-2 proteins in the CASP-commons experiment

Journal Article · Mon Aug 30 00:00:00 EDT 2021 · Proteins

DOI:https://doi.org/10.1002/prot.26231· OSTI ID:1976381

^[1]; ^[2]; Billings, Wendy M. ^[3]; ^[3]; ^[4]; Kwon, Sohee ^[5]; ^[6]; ^[5]; ^[6]; Won, Jonghun ^[5]

University of California, Davis, CA (United States); OSTI
University of Maryland, College Park, MD (United States)
Brigham Young University, Provo, UT (United States)
University of California, Davis, CA (United States)
Seoul National University, Seoul (Korea, Republic of)
Vilnius University (Lithuania)

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).

View Accepted Manuscript (DOE)

Research Organization:: Donald Danforth Plant Science Center, St. Louis, MO (United States); Georgia Institute of Technology, Atlanta, GA (United States)

Sponsoring Organization:: Biotechnology and Biological Science Research Council; Biotechnology and Biological Sciences Research Council (BBSRC); National Institutes of Health (NIH); National Research Foundation of Korea (NRF); National Science Centre (NCN); National Science Foundation (NSF); Research Council of Lithuania; USDOE; USDOE Office of Science (SC)

Contributing Organization:: CASP‐COVID participants

Grant/Contract Number:: SC0020400; SC0021303

OSTI ID:: 1976381

Alternate ID(s):: OSTI ID: 1824727

Journal Information:: Proteins, Journal Name: Proteins Journal Issue: 12 Vol. 89; ISSN 0887-3585

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

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