Critical assessment of methods of protein structure prediction (CASP)—Round XIV

Critical assessment of structure prediction (CASP) is a community experiment to advance methods of computing three‐dimensional protein structure from amino acid sequence. Core components are rigorous blind testing of methods and evaluation of the results by independent assessors. In the most recent...

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Published in:	Proteins, structure, function, and bioinformatics Vol. 89; no. 12; pp. 1607 - 1617
Main Authors:	Kryshtafovych, Andriy, Schwede, Torsten, Topf, Maya, Fidelis, Krzysztof, Moult, John
Format:	Journal Article
Language:	English
Published:	Hoboken, USA John Wiley & Sons, Inc 01.12.2021 Wiley Subscription Services, Inc
Subjects:	Alphafold Amino Acid Sequence Amino acids CASP community wide experiment Computational Biology Crystal structure Deep learning Model accuracy Models, Statistical Molecular Dynamics Simulation Predictions Protein Conformation Protein Folding Protein structure protein structure prediction Proteins Proteins - chemistry Proteins - metabolism Sequence Analysis, Protein Software Alphafold community wide experiment protein folding CASP protein structure prediction
ISSN:	0887-3585, 1097-0134, 1097-0134
Online Access:	Get full text
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Abstract	Critical assessment of structure prediction (CASP) is a community experiment to advance methods of computing three‐dimensional protein structure from amino acid sequence. Core components are rigorous blind testing of methods and evaluation of the results by independent assessors. In the most recent experiment (CASP14), deep‐learning methods from one research group consistently delivered computed structures rivaling the corresponding experimental ones in accuracy. In this sense, the results represent a solution to the classical protein‐folding problem, at least for single proteins. The models have already been shown to be capable of providing solutions for problematic crystal structures, and there are broad implications for the rest of structural biology. Other research groups also substantially improved performance. Here, we describe these results and outline some of the many implications. Other related areas of CASP, including modeling of protein complexes, structure refinement, estimation of model accuracy, and prediction of inter‐residue contacts and distances, are also described.
AbstractList	Critical assessment of structure prediction (CASP) is a community experiment to advance methods of computing three‐dimensional protein structure from amino acid sequence. Core components are rigorous blind testing of methods and evaluation of the results by independent assessors. In the most recent experiment (CASP14), deep‐learning methods from one research group consistently delivered computed structures rivaling the corresponding experimental ones in accuracy. In this sense, the results represent a solution to the classical protein‐folding problem, at least for single proteins. The models have already been shown to be capable of providing solutions for problematic crystal structures, and there are broad implications for the rest of structural biology. Other research groups also substantially improved performance. Here, we describe these results and outline some of the many implications. Other related areas of CASP, including modeling of protein complexes, structure refinement, estimation of model accuracy, and prediction of inter‐residue contacts and distances, are also described. CASP is a community experiment to advance methods of computing three-dimensional protein structure from amino acid sequence. Core components are rigorous blind testing of methods and evaluation of the results by independent assessors. In the most recent experiment (CASP14) deep learning methods from one research group consistently delivered computed structures rivalling the corresponding experimental ones in accuracy. In this sense, the results represent a solution to the classical protein folding problem, at least for single proteins. The models have already been shown to be capable of providing solutions for problematic crystal structures, and there are broad implications for the rest of structural biology. Other research groups also substantially improved performance. Here we describe these results and outline some of the many implications. Other related areas of CASP, including modeling of protein complexes, structure refinement, estimation of model accuracy, and prediction of inter-residue contacts and distances, are also described. Critical assessment of structure prediction (CASP) is a community experiment to advance methods of computing three-dimensional protein structure from amino acid sequence. Core components are rigorous blind testing of methods and evaluation of the results by independent assessors. In the most recent experiment (CASP14), deep-learning methods from one research group consistently delivered computed structures rivaling the corresponding experimental ones in accuracy. In this sense, the results represent a solution to the classical protein-folding problem, at least for single proteins. The models have already been shown to be capable of providing solutions for problematic crystal structures, and there are broad implications for the rest of structural biology. Other research groups also substantially improved performance. Here, we describe these results and outline some of the many implications. Other related areas of CASP, including modeling of protein complexes, structure refinement, estimation of model accuracy, and prediction of inter-residue contacts and distances, are also described.Critical assessment of structure prediction (CASP) is a community experiment to advance methods of computing three-dimensional protein structure from amino acid sequence. Core components are rigorous blind testing of methods and evaluation of the results by independent assessors. In the most recent experiment (CASP14), deep-learning methods from one research group consistently delivered computed structures rivaling the corresponding experimental ones in accuracy. In this sense, the results represent a solution to the classical protein-folding problem, at least for single proteins. The models have already been shown to be capable of providing solutions for problematic crystal structures, and there are broad implications for the rest of structural biology. Other research groups also substantially improved performance. Here, we describe these results and outline some of the many implications. Other related areas of CASP, including modeling of protein complexes, structure refinement, estimation of model accuracy, and prediction of inter-residue contacts and distances, are also described.
Author	Topf, Maya Schwede, Torsten Kryshtafovych, Andriy Fidelis, Krzysztof Moult, John
AuthorAffiliation	1 Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USA 3 Centre for Structural Systems Biology, Leibniz-Institut für Experimentelle Virologie and Universit tsklinikum Hamburg-Eppendorf (UKE), Hamburg, Germany 4 Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA, Department of Cell Biology and Molecular Genetics, University of Maryland 2 University of Basel, Biozentrum & SIB Swiss Institute of Bioinformatics, Basel, Switzerland
AuthorAffiliation_xml	– name: 1 Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USA – name: 3 Centre for Structural Systems Biology, Leibniz-Institut für Experimentelle Virologie and Universit tsklinikum Hamburg-Eppendorf (UKE), Hamburg, Germany – name: 2 University of Basel, Biozentrum & SIB Swiss Institute of Bioinformatics, Basel, Switzerland – name: 4 Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA, Department of Cell Biology and Molecular Genetics, University of Maryland
Author_xml	– sequence: 1 givenname: Andriy orcidid: 0000-0001-5066-7178 surname: Kryshtafovych fullname: Kryshtafovych, Andriy organization: Genome Center, University of California, Davis – sequence: 2 givenname: Torsten orcidid: 0000-0003-2715-335X surname: Schwede fullname: Schwede, Torsten organization: University of Basel, Biozentrum & SIB Swiss Institute of Bioinformatics – sequence: 3 givenname: Maya orcidid: 0000-0002-8185-1215 surname: Topf fullname: Topf, Maya organization: Centre for Structural Systems Biology, Leibniz‐Institut für Experimentelle Virologie and Universit tsklinikum Hamburg‐Eppendorf (UKE) – sequence: 4 givenname: Krzysztof orcidid: 0000-0002-8061-412X surname: Fidelis fullname: Fidelis, Krzysztof organization: Genome Center, University of California, Davis – sequence: 5 givenname: John orcidid: 0000-0002-3012-2282 surname: Moult fullname: Moult, John email: jmoult@umd.edu organization: University of Maryland
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/34533838$$D View this record in MEDLINE/PubMed
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Snippet	Critical assessment of structure prediction (CASP) is a community experiment to advance methods of computing three‐dimensional protein structure from amino... Critical assessment of structure prediction (CASP) is a community experiment to advance methods of computing three-dimensional protein structure from amino... CASP is a community experiment to advance methods of computing three-dimensional protein structure from amino acid sequence. Core components are rigorous blind...
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SubjectTerms	Alphafold Amino Acid Sequence Amino acids CASP community wide experiment Computational Biology Crystal structure Deep learning Model accuracy Models, Statistical Molecular Dynamics Simulation Predictions Protein Conformation Protein Folding Protein structure protein structure prediction Proteins Proteins - chemistry Proteins - metabolism Sequence Analysis, Protein Software
Title	Critical assessment of methods of protein structure prediction (CASP)—Round XIV
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