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Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM

2001; Wiley; Volume: 45; Issue: S5 Linguagem: Inglês

10.1002/prot.1168

1097-0134

Paul A. Bates, Lawrence A. Kelley, Robert M. MacCallum, Michael J.E. Sternberg,

Microbial Metabolic Engineering and Bioproduction

Proteins: Structure, Function, and BioinformaticsVolume 45, Issue S5 p. 39-46 Comparative Modeling: Prediction Report Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM Paul A. Bates, Corresponding Author Paul A. Bates paul.bates@ICRF.icnet.uk Biomolecular Modelling Laboratory, Imperial Cancer Research Fund, London, United Kingdom Paul Bates and Lawrence Kelley contributed equally to this work.Biomolecular Modelling Laboratory, Imperial Cancer Research Fund, 44 Lincoln's Inn Fields, London WC2A 3PX, UK===Search for more papers by this authorLawrence A. Kelley, Lawrence A. Kelley Biomolecular Modelling Laboratory, Imperial Cancer Research Fund, London, United Kingdom Paul Bates and Lawrence Kelley contributed equally to this work.Search for more papers by this authorRobert M. MacCallum, Robert M. MacCallum Biomolecular Modelling Laboratory, Imperial Cancer Research Fund, London, United KingdomSearch for more papers by this authorMichael J.E. Sternberg, Corresponding Author Michael J.E. Sternberg m.sternberg@ICRF.icnet.uk Biomolecular Modelling Laboratory, Imperial Cancer Research Fund, London, United KingdomBiomolecular Modelling Laboratory, Imperial Cancer Research Fund, 44 Lincoln's Inn Fields, London WC2A 3PX, UK===Search for more papers by this author Paul A. Bates, Corresponding Author Paul A. Bates paul.bates@ICRF.icnet.uk Biomolecular Modelling Laboratory, Imperial Cancer Research Fund, London, United Kingdom Paul Bates and Lawrence Kelley contributed equally to this work.Biomolecular Modelling Laboratory, Imperial Cancer Research Fund, 44 Lincoln's Inn Fields, London WC2A 3PX, UK===Search for more papers by this authorLawrence A. Kelley, Lawrence A. Kelley Biomolecular Modelling Laboratory, Imperial Cancer Research Fund, London, United Kingdom Paul Bates and Lawrence Kelley contributed equally to this work.Search for more papers by this authorRobert M. MacCallum, Robert M. MacCallum Biomolecular Modelling Laboratory, Imperial Cancer Research Fund, London, United KingdomSearch for more papers by this authorMichael J.E. Sternberg, Corresponding Author Michael J.E. Sternberg m.sternberg@ICRF.icnet.uk Biomolecular Modelling Laboratory, Imperial Cancer Research Fund, London, United KingdomBiomolecular Modelling Laboratory, Imperial Cancer Research Fund, 44 Lincoln's Inn Fields, London WC2A 3PX, UK===Search for more papers by this author First published: 28 January 2002 https://doi.org/10.1002/prot.1168Citations: 381 Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Abstract Fourteen models were constructed and analyzed for the comparative modeling section of Critical Assessment of Techniques for Protein Structure Prediction (CASP4). Sequence identity between each target and the best possible parent(s) ranged between 55 and 13%, and the root-mean-square deviation between model and target was from 0.8 to 17.9 Å. In the fold recognition section, 10 of the 11 remote homologues were recognized. The modeling protocols are a combination of automated computer algorithms, 3D-JIGSAW (for comparative modeling) and 3D-PSSM (for fold recognition), with human intervention at certain critical stages. In particular, intervention is required to check superfamily assignment, best possible parents from which to model, sequence alignments to those parents and take-off regions for modeling variable regions. There now is a convergence of algorithms for comparative modeling and fold recognition, particularly in the region of remote homology. Proteins 2001;Suppl 5:39–46. © 2002 Wiley-Liss, Inc. Citing Literature Volume45, IssueS5Supplement: Fourth Meeting on the Critical Assessment of Techniques for Protein Structure Prediction2001Pages 39-46 RelatedInformation