Protein structure prediction center in CASP8

被引:20
作者
Kryshtafovych, Andriy [1 ]
Krysko, Oleh [1 ]
Daniluk, Pawel [1 ]
Dmytriv, Zinovii [1 ]
Fidelis, Krzysztof [1 ]
机构
[1] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA
关键词
CASP; protein structure prediction;
D O I
10.1002/prot.22517
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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.
引用
收藏
页码:5 / 9
页数:5
相关论文
共 10 条
[1]   Evaluation of template-based models in CASP8 with standard measures [J].
Cozzetto, Domenico ;
Kryshtafovych, Andriy ;
Fidelis, Krzysztof ;
Moult, John ;
Rost, Burkhard ;
Tramontano, Anna .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2009, 77 :18-28
[2]   Searching protein structure databases with DaliLite v.3 [J].
Holm, L. ;
Kaariainen, S. ;
Rosenstrom, P. ;
Schenkel, A. .
BIOINFORMATICS, 2008, 24 (23) :2780-2781
[3]   CASP6 data processing and automatic evaluation at the protein structure prediction center [J].
Kryshtafovych, A ;
Milostan, M ;
Szajkowski, L ;
Daniluk, P ;
Fidelis, K .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2005, 61 :19-23
[4]   New tools and expanded data analysis capabilities at the protein structure prediction center [J].
Kryshtafovych, Andriy ;
Prlic, Andreas ;
Dmytriv, Zinoviy ;
Daniluk, Pawel ;
Milostan, Maciej ;
Eyrich, Volker ;
Hubbard, Tim ;
Fidelis, Krzysztof .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2007, 69 :19-26
[5]   MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison [J].
Ortiz, AR ;
Strauss, CEM ;
Olmea, O .
PROTEIN SCIENCE, 2002, 11 (11) :2606-2621
[6]   Adding some SPICE to DAS [J].
Prlic, A ;
Down, TA ;
Hubbard, TJP .
BIOINFORMATICS, 2005, 21 :40-41
[7]   RASMOL - BIOMOLECULAR GRAPHICS FOR ALL [J].
SAYLE, RA ;
MILNERWHITE, EJ .
TRENDS IN BIOCHEMICAL SCIENCES, 1995, 20 (09) :374-376
[8]   Target domain definition and classification in CASP8 [J].
Tress, Michael L. ;
Ezkurdia, Iakes ;
Richardson, Jane S. .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2009, 77 :10-17
[9]  
Zemla A, 2001, PROTEINS, P13
[10]   LGA: a method for finding 3D similarities in protein structures [J].
Zemla, A .
NUCLEIC ACIDS RESEARCH, 2003, 31 (13) :3370-3374