Literature DB >> 17918728

Progress from CASP6 to CASP7.

Andriy Kryshtafovych1, Krzysztof Fidelis, John Moult.   

Abstract

This article describes the general quality of models of three dimensional structure submitted to CASP7 and analyzes progress since the previous experiment, primarily using measures that were used in earlier analyses. Overall improvement in model accuracy compared to CASP6 is modest, but there are two developments of note: server performance has moved closer to that of humans, and there has been a significant improvement in the fraction of targets for which the best model is superior to that obtainable using knowledge of a single best template structure. (c) 2007 Wiley-Liss, Inc.

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Year:  2007        PMID: 17918728     DOI: 10.1002/prot.21769

Source DB:  PubMed          Journal:  Proteins        ISSN: 0887-3585


  29 in total

1.  Relative packing groups in template-based structure prediction: cooperative effects of true positive constraints.

Authors:  Ryan Day; Xiaotao Qu; Rosemarie Swanson; Zach Bohannan; Robert Bliss; Jerry Tsai
Journal:  J Comput Biol       Date:  2011-01       Impact factor: 1.479

Review 2.  FINDSITE: a combined evolution/structure-based approach to protein function prediction.

Authors:  Jeffrey Skolnick; Michal Brylinski
Journal:  Brief Bioinform       Date:  2009-03-26       Impact factor: 11.622

3.  Protein structure homology modeling using SWISS-MODEL workspace.

Authors:  Lorenza Bordoli; Florian Kiefer; Konstantin Arnold; Pascal Benkert; James Battey; Torsten Schwede
Journal:  Nat Protoc       Date:  2009       Impact factor: 13.491

4.  Use of decoys to optimize an all-atom force field including hydration.

Authors:  Yelena A Arnautova; Harold A Scheraga
Journal:  Biophys J       Date:  2008-05-23       Impact factor: 4.033

5.  The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models.

Authors:  Daniel A Keedy; Christopher J Williams; Jeffrey J Headd; W Bryan Arendall; Vincent B Chen; Gary J Kapral; Robert A Gillespie; Jeremy N Block; Adam Zemla; David C Richardson; Jane S Richardson
Journal:  Proteins       Date:  2009

6.  Outcome of a workshop on applications of protein models in biomedical research.

Authors:  Torsten Schwede; Andrej Sali; Barry Honig; Michael Levitt; Helen M Berman; David Jones; Steven E Brenner; Stephen K Burley; Rhiju Das; Nikolay V Dokholyan; Roland L Dunbrack; Krzysztof Fidelis; Andras Fiser; Adam Godzik; Yuanpeng Janet Huang; Christine Humblet; Matthew P Jacobson; Andrzej Joachimiak; Stanley R Krystek; Tanja Kortemme; Andriy Kryshtafovych; Gaetano T Montelione; John Moult; Diana Murray; Roberto Sanchez; Tobin R Sosnick; Daron M Standley; Terry Stouch; Sandor Vajda; Max Vasquez; John D Westbrook; Ian A Wilson
Journal:  Structure       Date:  2009-02-13       Impact factor: 5.006

7.  Improved estimation of structure predictor quality.

Authors:  Kevin W DeRonne; George Karypis
Journal:  BMC Struct Biol       Date:  2009-06-30

Review 8.  Protein function annotation by homology-based inference.

Authors:  Yaniv Loewenstein; Domenico Raimondo; Oliver C Redfern; James Watson; Dmitrij Frishman; Michal Linial; Christine Orengo; Janet Thornton; Anna Tramontano
Journal:  Genome Biol       Date:  2009-02-02       Impact factor: 13.583

Review 9.  Folding by numbers: primary sequence statistics and their use in studying protein folding.

Authors:  Brent Wathen; Zongchao Jia
Journal:  Int J Mol Sci       Date:  2009-04-08       Impact factor: 6.208

10.  Critical assessment of methods of protein structure prediction-Round VII.

Authors:  John Moult; Krzysztof Fidelis; Andriy Kryshtafovych; Burkhard Rost; Tim Hubbard; Anna Tramontano
Journal:  Proteins       Date:  2007
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