دورية أكاديمية
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A structural biology community assessment of AlphaFold2 applications.

التفاصيل البيبلوغرافية
العنوان: A structural biology community assessment of AlphaFold2 applications.
المؤلفون: Akdel M; Bioinformatics Group, Department of Plant Sciences, Wageningen University and Research, Wageningen, the Netherlands., Pires DEV; School of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia., Pardo EP; Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain.; Barcelona Supercomputing Center (BSC), Barcelona, Spain., Jänes J; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK., Zalevsky AO; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation., Mészáros B; European Molecular Biology Laboratory, Heidelberg, Germany., Bryant P; Dep of Biochemistry and Biophysics and Science for Life Laboratory, Solna, Sweden., Good LL; Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark., Laskowski RA; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK., Pozzati G; Dep of Biochemistry and Biophysics and Science for Life Laboratory, Solna, Sweden., Shenoy A; Dep of Biochemistry and Biophysics and Science for Life Laboratory, Solna, Sweden., Zhu W; Dep of Biochemistry and Biophysics and Science for Life Laboratory, Solna, Sweden., Kundrotas P; Dep of Biochemistry and Biophysics and Science for Life Laboratory, Solna, Sweden., Serra VR; Barcelona Supercomputing Center (BSC), Barcelona, Spain., Rodrigues CHM; School of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia., Dunham AS; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK., Burke D; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK., Borkakoti N; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK., Velankar S; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK., Frost A; Department of Biochemistry and Biophysics University of California, San Francisco, CA, USA., Basquin J; Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany., Lindorff-Larsen K; Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark., Bateman A; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK., Kajava AV; Université de Montpellier, Centre de Recherche en Biologie Cellulaire de Montpellier (CRBM) CNRS, Montpellier, France., Valencia A; Barcelona Supercomputing Center (BSC), Barcelona, Spain. alfonso.valencia@bsc.es., Ovchinnikov S; Faculty of Arts and Sciences, Division of Science, Harvard University, Cambridge, MA, USA. so@fas.harvard.edu., Durairaj J; Biozentrum, University of Basel, Basel, Switzerland. janani.durairaj@gmail.com., Ascher DB; School of Chemistry and Molecular Biology, University of Queensland, Brisbane, Queensland, Australia. d.ascher@uq.edu.au., Thornton JM; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK. thornton@ebi.ac.uk., Davey NE; Institute of Cancer Research, London, UK. norman.davey@icr.ac.uk., Stein A; Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark. amelie.stein@bio.ku.dk., Elofsson A; Dep of Biochemistry and Biophysics and Science for Life Laboratory, Solna, Sweden. arne@bioinfo.se., Croll TI; Cambridge Institute for Medical Research, Department of Haematology, The University of Cambridge, Cambridge, UK. tic20@cam.ac.uk., Beltrao P; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK. pbeltrao@ethz.ch.; Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland. pbeltrao@ethz.ch.
المصدر: Nature structural & molecular biology [Nat Struct Mol Biol] 2022 Nov; Vol. 29 (11), pp. 1056-1067. Date of Electronic Publication: 2022 Nov 07.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Nature Pub. Group Country of Publication: United States NLM ID: 101186374 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1545-9985 (Electronic) Linking ISSN: 15459985 NLM ISO Abbreviation: Nat Struct Mol Biol Subsets: MEDLINE
أسماء مطبوعة: Original Publication: New York : Nature Pub. Group, c2004-
مواضيع طبية MeSH: Computational Biology*/methods , Furylfuramide*, Binding Sites ; Proteins/chemistry ; Databases, Protein ; Protein Conformation
مستخلص: Most proteins fold into 3D structures that determine how they function and orchestrate the biological processes of the cell. Recent developments in computational methods for protein structure predictions have reached the accuracy of experimentally determined models. Although this has been independently verified, the implementation of these methods across structural-biology applications remains to be tested. Here, we evaluate the use of AlphaFold2 (AF2) predictions in the study of characteristic structural elements; the impact of missense variants; function and ligand binding site predictions; modeling of interactions; and modeling of experimental structural data. For 11 proteomes, an average of 25% additional residues can be confidently modeled when compared with homology modeling, identifying structural features rarely seen in the Protein Data Bank. AF2-based predictions of protein disorder and complexes surpass dedicated tools, and AF2 models can be used across diverse applications equally well compared with experimentally determined structures, when the confidence metrics are critically considered. In summary, we find that these advances are likely to have a transformative impact in structural biology and broader life-science research.
(© 2022. The Author(s).)
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معلومات مُعتمدة: United Kingdom WT_ Wellcome Trust; 28159 United Kingdom CRUK_ Cancer Research UK; DP5 OD026389 United States OD NIH HHS; R21 AI156595 United States AI NIAID NIH HHS
المشرفين على المادة: 054NR2135Y (Furylfuramide)
0 (Proteins)
تواريخ الأحداث: Date Created: 20221107 Date Completed: 20221116 Latest Revision: 20240421
رمز التحديث: 20240421
مُعرف محوري في PubMed: PMC9663297
DOI: 10.1038/s41594-022-00849-w
PMID: 36344848
قاعدة البيانات: MEDLINE
الوصف
تدمد:1545-9985
DOI:10.1038/s41594-022-00849-w