Literature DB >> 19722263

Protein structure prediction center in CASP8.

Andriy Kryshtafovych1, Oleh Krysko, Pawel Daniluk, Zinovii Dmytriv, Krzysztof Fidelis.   

Abstract

We present an outline of the Critical Assessment of Protein Structure Prediction (CASP) infrastructure implemented at the University of California, Davis, Protein Structure Prediction Center. The infrastructure supports selection and validation of prediction targets, collection of predictions, standard evaluation of submitted predictions, and presentation of results. The Center also supports information exchange relating to CASP experiments and structure prediction in general. Technical aspects of conducting the CASP8 experiment and relevant statistics are also provided. Copyright 2009 Wiley-Liss, Inc.

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Year:  2009        PMID: 19722263      PMCID: PMC2863353          DOI: 10.1002/prot.22517

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


  10 in total

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4.  Adding some SPICE to DAS.

Authors:  Andreas Prlić; Thomas A Down; Tim J P Hubbard
Journal:  Bioinformatics       Date:  2005-09-01       Impact factor: 6.937

5.  CASP6 data processing and automatic evaluation at the protein structure prediction center.

Authors:  Andriy Kryshtafovych; Maciej Milostan; Lukasz Szajkowski; Pawel Daniluk; Krzysztof Fidelis
Journal:  Proteins       Date:  2005

6.  RASMOL: biomolecular graphics for all.

Authors:  R A Sayle; E J Milner-White
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7.  Target domain definition and classification in CASP8.

Authors:  Michael L Tress; Iakes Ezkurdia; Jane S Richardson
Journal:  Proteins       Date:  2009

8.  Evaluation of template-based models in CASP8 with standard measures.

Authors:  Domenico Cozzetto; Andriy Kryshtafovych; Krzysztof Fidelis; John Moult; Burkhard Rost; Anna Tramontano
Journal:  Proteins       Date:  2009

9.  Searching protein structure databases with DaliLite v.3.

Authors:  L Holm; S Kääriäinen; P Rosenström; A Schenkel
Journal:  Bioinformatics       Date:  2008-09-25       Impact factor: 6.937

10.  New tools and expanded data analysis capabilities at the Protein Structure Prediction Center.

Authors:  Andriy Kryshtafovych; Andreas Prlic; Zinoviy Dmytriv; Pawel Daniluk; Maciej Milostan; Volker Eyrich; Tim Hubbard; Krzysztof Fidelis
Journal:  Proteins       Date:  2007
  10 in total
  21 in total

1.  TASSER_WT: a protein structure prediction algorithm with accurate predicted contact restraints for difficult protein targets.

Authors:  Seung Yup Lee; Jeffrey Skolnick
Journal:  Biophys J       Date:  2010-11-03       Impact factor: 4.033

2.  Novel proteases from the genome of the carnivorous plant Drosera capensis: Structural prediction and comparative analysis.

Authors:  Carter T Butts; Jan C Bierma; Rachel W Martin
Journal:  Proteins       Date:  2016-07-13

Review 3.  MOLS sampling and its applications in structural biophysics.

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4.  CASP11 statistics and the prediction center evaluation system.

Authors:  Andriy Kryshtafovych; Bohdan Monastyrskyy; Krzysztof Fidelis
Journal:  Proteins       Date:  2016-03-09

5.  PROTS: a fragment based protein thermo-stability potential.

Authors:  Yunqi Li; Jian Zhang; David Tai; C Russell Middaugh; Yang Zhang; Jianwen Fang
Journal:  Proteins       Date:  2011-10-05

6.  Assessment of template-based protein structure predictions in CASP10.

Authors:  Yuanpeng J Huang; Binchen Mao; James M Aramini; Gaetano T Montelione
Journal:  Proteins       Date:  2014-02

7.  Generating reservoir conformations for replica exchange through the use of the conformational space annealing method.

Authors:  Asim Okur; Benjamin T Miller; Keehyoung Joo; Jooyoung Lee; Bernard R Brooks
Journal:  J Chem Theory Comput       Date:  2013-02-01       Impact factor: 6.006

8.  MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8.

Authors:  Zheng Wang; Jesse Eickholt; Jianlin Cheng
Journal:  Bioinformatics       Date:  2010-02-11       Impact factor: 6.937

9.  Evaluation of template-based models in CASP8 with standard measures.

Authors:  Domenico Cozzetto; Andriy Kryshtafovych; Krzysztof Fidelis; John Moult; Burkhard Rost; Anna Tramontano
Journal:  Proteins       Date:  2009

10.  Evaluation of the template-based modeling in CASP12.

Authors:  Andriy Kryshtafovych; Bohdan Monastyrskyy; Krzysztof Fidelis; John Moult; Torsten Schwede; Anna Tramontano
Journal:  Proteins       Date:  2017-12-04
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