Critical assessment of methods of protein structure prediction (CASP)—Round XII
This article reports the outcome of the 12th round of Critical Assessment of Structure Prediction (CASP12), held in 2016. CASP is a community experiment to determine the state of the art in modeling protein structure from amino acid sequence. Participants are provided sequence information and in tur...
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| Vydáno v: | Proteins, structure, function, and bioinformatics Ročník 86; číslo S1; s. 7 - 15 |
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| Hlavní autoři: | , , , , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
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United States
Wiley Subscription Services, Inc
01.03.2018
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| ISSN: | 0887-3585, 1097-0134, 1097-0134 |
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| Abstract | This article reports the outcome of the 12th round of Critical Assessment of Structure Prediction (CASP12), held in 2016. CASP is a community experiment to determine the state of the art in modeling protein structure from amino acid sequence. Participants are provided sequence information and in turn provide protein structure models and related information. Analysis of the submitted structures by independent assessors provides a comprehensive picture of the capabilities of current methods, and allows progress to be identified. This was again an exciting round of CASP, with significant advances in 4 areas: (i) The use of new methods for predicting three‐dimensional contacts led to a two‐fold improvement in contact accuracy. (ii) As a consequence, model accuracy for proteins where no template was available improved dramatically. (iii) Models based on a structural template showed overall improvement in accuracy. (iv) Methods for estimating the accuracy of a model continued to improve. CASP continued to develop new areas: (i) Assessing methods for building quaternary structure models, including an expansion of the collaboration between CASP and CAPRI. (ii) Modeling with the aid of experimental data was extended to include SAXS data, as well as again using chemical cross‐linking information. (iii) A team of assessors evaluated the suitability of models for a range of applications, including mutation interpretation, analysis of ligand binding properties, and identification of interfaces. This article describes the experiment and summarizes the results. The rest of this special issue of PROTEINS contains papers describing CASP12 results and assessments in more detail. |
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| AbstractList | This article reports the outcome of the 12th round of Critical Assessment of Structure Prediction (CASP12), held in 2016. CASP is a community experiment to determine the state of the art in modeling protein structure from amino acid sequence. Participants are provided sequence information and in turn provide protein structure models and related information. Analysis of the submitted structures by independent assessors provides a comprehensive picture of the capabilities of current methods, and allows progress to be identified. This was again an exciting round of CASP, with significant advances in 4 areas: (i) The use of new methods for predicting three‐dimensional contacts led to a two‐fold improvement in contact accuracy. (ii) As a consequence, model accuracy for proteins where no template was available improved dramatically. (iii) Models based on a structural template showed overall improvement in accuracy. (iv) Methods for estimating the accuracy of a model continued to improve. CASP continued to develop new areas: (i) Assessing methods for building quaternary structure models, including an expansion of the collaboration between CASP and CAPRI. (ii) Modeling with the aid of experimental data was extended to include SAXS data, as well as again using chemical cross‐linking information. (iii) A team of assessors evaluated the suitability of models for a range of applications, including mutation interpretation, analysis of ligand binding properties, and identification of interfaces. This article describes the experiment and summarizes the results. The rest of this special issue of PROTEINS contains papers describing CASP12 results and assessments in more detail. This article reports the outcome of the 12th round of Critical Assessment of Structure Prediction (CASP12), held in 2016. CASP is a community experiment to determine the state of the art in modeling protein structure from amino acid sequence. Participants are provided sequence information and in turn provide protein structure models and related information. Analysis of the submitted structures by independent assessors provides a comprehensive picture of the capabilities of current methods, and allows progress to be identified. This was again an exciting round of CASP, with significant advances in 4 areas: (i) The use of new methods for predicting three-dimensional contacts led to a two-fold improvement in contact accuracy. (ii) As a consequence, model accuracy for proteins where no template was available improved dramatically. (iii) Models based on a structural template showed overall improvement in accuracy. (iv) Methods for estimating the accuracy of a model continued to improve. CASP continued to develop new areas: (i) Assessing methods for building quaternary structure models, including an expansion of the collaboration between CASP and CAPRI. (ii) Modeling with the aid of experimental data was extended to include SAXS data, as well as again using chemical cross-linking information. (iii) A team of assessors evaluated the suitability of models for a range of applications, including mutation interpretation, analysis of ligand binding properties, and identification of interfaces. This article describes the experiment and summarizes the results. The rest of this special issue of PROTEINS contains papers describing CASP12 results and assessments in more detail.This article reports the outcome of the 12th round of Critical Assessment of Structure Prediction (CASP12), held in 2016. CASP is a community experiment to determine the state of the art in modeling protein structure from amino acid sequence. Participants are provided sequence information and in turn provide protein structure models and related information. Analysis of the submitted structures by independent assessors provides a comprehensive picture of the capabilities of current methods, and allows progress to be identified. This was again an exciting round of CASP, with significant advances in 4 areas: (i) The use of new methods for predicting three-dimensional contacts led to a two-fold improvement in contact accuracy. (ii) As a consequence, model accuracy for proteins where no template was available improved dramatically. (iii) Models based on a structural template showed overall improvement in accuracy. (iv) Methods for estimating the accuracy of a model continued to improve. CASP continued to develop new areas: (i) Assessing methods for building quaternary structure models, including an expansion of the collaboration between CASP and CAPRI. (ii) Modeling with the aid of experimental data was extended to include SAXS data, as well as again using chemical cross-linking information. (iii) A team of assessors evaluated the suitability of models for a range of applications, including mutation interpretation, analysis of ligand binding properties, and identification of interfaces. This article describes the experiment and summarizes the results. The rest of this special issue of PROTEINS contains papers describing CASP12 results and assessments in more detail. This article reports the outcome of the 12th round of Critical Assessment of Structure Prediction (CASP12), held in 2016. CASP is a community experiment to determine the state of the art in modeling protein structure from amino acid sequence. Participants are provided sequence information and in turn provide protein structure models and related information. Analysis of the submitted structures by independent assessors provides a comprehensive picture of the capabilities of current methods, and allows progress to be identified. This was again an exciting round of CASP, with significant advances in 4 areas: (i) The use of new methods for predicting three‐dimensional contacts led to a two‐fold improvement in contact accuracy. (ii) As a consequence, model accuracy for proteins where no template was available improved dramatically. (iii) Models based on a structural template showed overall improvement in accuracy. (iv) Methods for estimating the accuracy of a model continued to improve. CASP continued to develop new areas: (i) Assessing methods for building quaternary structure models, including an expansion of the collaboration between CASP and CAPRI. (ii) Modeling with the aid of experimental data was extended to include SAXS data, as well as again using chemical cross‐linking information. (iii) A team of assessors evaluated the suitability of models for a range of applications, including mutation interpretation, analysis of ligand binding properties, and identification of interfaces. This article describes the experiment and summarizes the results. The rest of this special issue of PROTEINS contains papers describing CASP12 results and assessments in more detail. This paper reports the outcome of the 12th round of Critical Assessment of Structure Prediction (CASP12), held in 2016. CASP is a community experiment to determine the state of the art in modeling protein structure from amino acid sequence. Participants are provided sequence information and in turn provide protein structure models and related information. Analysis of the submitted structures by independent assessors provides a comprehensive picture of the capabilities of current methods, and allows progress to be identified. This was again an exciting round of CASP, with significant advances in four areas: (i) The use of new methods for predicting three dimensional contacts led to a two-fold improvement in contact accuracy. (ii) As a consequence, model accuracy for proteins where no template was available improved dramatically. (iii) Models based on a structural template showed overall improvement in accuracy. (iv) Methods for estimating the accuracy of a model continued to improve. CASP continued to develop new areas: (i) Assessing methods for building quaternary structure models, including an expansion of the collaboration between CASP and CAPRI. (ii) Modeling with the aid of experimental data was extended to include SAXS data, as well as again using chemical crosslinking information. (iii) A team of assessors evaluated the suitability of models for a range of applications, including mutation interpretation, analysis of ligand binding properties, and identification of interfaces. This paper describes the experiment and summarizes the results. The rest of this special issue of PROTEINS contains papers describing CASP12 results and assessments in more detail. |
| Author | Schwede, Torsten Tramontano, Anna Kryshtafovych, Andriy Moult, John Fidelis, Krzysztof |
| AuthorAffiliation | University of Basel, Biozentrum & SIB Swiss Institute of Bioinformatics, Basel, Switzerland Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USA Institute for Bioscience and Biotechnology Research and Department of Cell Biology and Molecular Genetics, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA Department of Physics and Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza University of Rome, P.le Aldo Moro, 5, 00185 Rome, Italy |
| AuthorAffiliation_xml | – name: Institute for Bioscience and Biotechnology Research and Department of Cell Biology and Molecular Genetics, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA – name: Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USA – name: University of Basel, Biozentrum & SIB Swiss Institute of Bioinformatics, Basel, Switzerland – name: Department of Physics and Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza University of Rome, P.le Aldo Moro, 5, 00185 Rome, Italy |
| Author_xml | – sequence: 1 givenname: John orcidid: 0000-0002-3012-2282 surname: Moult fullname: Moult, John email: jmoult@umd.edu organization: Institute for Bioscience and Biotechnology Research and Department of Cell Biology and Molecular Genetics, University of Maryland, 9600 Gudelsky Drive – sequence: 2 givenname: Krzysztof orcidid: 0000-0002-8061-412X surname: Fidelis fullname: Fidelis, Krzysztof organization: Genome Center, University of California, Davis, 451 Health Sciences Drive – sequence: 3 givenname: Andriy orcidid: 0000-0001-5066-7178 surname: Kryshtafovych fullname: Kryshtafovych, Andriy organization: Genome Center, University of California, Davis, 451 Health Sciences Drive – sequence: 4 givenname: Torsten orcidid: 0000-0003-2715-335X surname: Schwede fullname: Schwede, Torsten organization: University of Basel, Biozentrum & SIB Swiss Institute of Bioinformatics – sequence: 5 givenname: Anna surname: Tramontano fullname: Tramontano, Anna organization: Sapienza University of Rome, P.le Aldo Moro, 5 |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/29082672$$D View this record in MEDLINE/PubMed |
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| SubjectTerms | Accuracy Amino acid sequence Amino acids CASP community wide experiment Computational Biology - methods Construction methods Humans Identification methods Interfaces Mathematical models Model accuracy Modelling Models, Molecular Models, Statistical Predictions Protein Conformation Protein structure protein structure prediction Proteins Proteins - chemistry Quaternary structure X-Ray Diffraction |
| Title | Critical assessment of methods of protein structure prediction (CASP)—Round XII |
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