CASP8 results in context of previous experiments

被引:28
作者
Kryshtafovych, Andriy [1 ]
Fidelis, Krzysztof [1 ]
Moult, John [2 ]
机构
[1] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA
[2] Univ Maryland, Inst Biotechnol, Ctr Adv Res Biotechnol, Rockville, MD 20850 USA
关键词
protein structure prediction; community wide experiment; CASP; progress; PROTEIN; PROGRESS; QUALITY; MODELS;
D O I
10.1002/prot.22562
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
The quality of structure models submitted to CASP8 is analyzed in the context of previous CASPs. To compare models from the latest experiment with their predecessors, we use the approaches consistent with the previous articles in this series. Using the basic evaluation measures accepted in CASP, there were no noticeable advances in the quality of the methods in any of the target difficulty categories. At the same time, there were three positive developments: (1) for set of the best models on each target, CASP8 registered the highest number of cases from all CASPs where alignment accuracy exceeded the maximum possible from the best template; (2) modeling accuracy of regions not present in the best template has improved; and (3) the loss in modeling quality from selection of nonoptimal models as the best ones submitted on the target has decreased.
引用
收藏
页码:217 / 228
页数:12
相关论文
共 13 条
[1]   Assessment of CASP8 structure predictions for template free targets [J].
Ben-David, Moshe ;
Noivirt-Brik, Orly ;
Paz, Aviv ;
Prilusky, Jaime ;
Sussman, Joel L. ;
Levy, Yaakov .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2009, 77 :50-65
[2]   Relationship between multiple sequence alignments and quality of protein comparative models [J].
Cozzetto, D ;
Tramontano, A .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2005, 58 (01) :151-157
[3]   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
[4]   The other 90% of the protein: Assessment beyond the Cαs for CASP8 template-based and high-accuracy models [J].
Keedy, Daniel A. ;
Williams, Christopher J. ;
Headd, Jeffrey J. ;
Arendall, W. Bryan, III ;
Chen, Vincent B. ;
Kapral, Gary J. ;
Gillespie, Robert A. ;
Block, Jeremy N. ;
Zemla, Adam ;
Richardson, David C. ;
Richardson, Jane S. .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2009, 77 :29-49
[5]   Progress over the first decade of CASP experiments [J].
Kryshtafovych, A ;
Venclovas, C ;
Fidelis, K ;
Moult, J .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2005, 61 :225-236
[6]   Progress from CASP6 to CASP7 [J].
Kryshtafovych, Andriy ;
Fidelis, Krzysztof ;
Moult, John .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2007, 69 :194-207
[7]   Using multiple templates to improve quality of homology models in automated homology modeling [J].
Larsson, Per ;
Wallner, Bjoern ;
Lindahl, Erik ;
Elofsson, Arne .
PROTEIN SCIENCE, 2008, 17 (06) :990-1002
[8]   Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features [J].
Lassmann, Timo ;
Frings, Oliver ;
Sonnhammer, Erik L. L. .
NUCLEIC ACIDS RESEARCH, 2009, 37 (03) :858-865
[9]   Outcome of a Workshop on Applications of Protein Models in Biomedical Research [J].
Schwede, Torsten ;
Sali, Andrej ;
Honig, Barry ;
Levitt, Michael ;
Berman, Helen M. ;
Jones, David ;
Brenner, Steven E. ;
Burley, Stephen K. ;
Das, Rhiju ;
Dokholyan, Nikolay V. ;
Dunbrack, Roland L., Jr. ;
Fidelis, Krzysztof ;
Fiser, Andras ;
Godzik, Adam ;
Huang, Yuanpeng Janet ;
Humblet, Christine ;
Jacobson, Matthew P. ;
Joachimiak, Andrzej ;
Krystek, Stanley R., Jr. ;
Kortemme, Tanja ;
Kryshtafovych, Andriy ;
Montelione, Gaetano T. ;
Moult, John ;
Murray, Diana ;
Sanchez, Roberto ;
Sosnick, Tobin R. ;
Standley, Daron M. ;
Stouch, Terry ;
Vajda, Sandor ;
Vasquez, Max ;
Westbrook, John D. ;
Wilson, Ian A. .
STRUCTURE, 2009, 17 (02) :151-159
[10]   Assessment of progress over the CASP experiments [J].
Venclovas, C ;
Zemla, A ;
Fidelis, K ;
Moult, J .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2003, 53 :585-595