CASP10 results compared to those of previous CASP experiments

被引:76
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 Biosci & Biotechnol Res, Dept Cell Biol & Mol Genet, Rockville, MD 20850 USA
关键词
PROTEIN-STRUCTURE PREDICTION; HOMOLOGY DETECTION; PROGRESS; BOTTLENECKS; DECADE;
D O I
10.1002/prot.24448
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 compare results of the community efforts in modeling protein structures in the tenth CASP experiment, with those in earlier CASPs particularly in CASP5, a decade ago. There is a substantial improvement in template based model accuracy as reflected in more successful modeling of regions of structure not easily derived from a single experimental structure template, most likely reflecting intensive work within the modeling community in developing methods that make use of multiple templates, as well as the increased number of experimental structures available. Deriving structural information not obvious from a template is the most demanding as well as one of the most useful tasks that modeling can perform. Thus this is gratifying progress. By contrast, overall backbone accuracy of models appears little changed in the last decade. This puzzling result is explained by two factors-increased database size in some ways makes it harder to choose the best available templates, and the increased intrinsic difficulty of CASP targets as experimental work has progressed to larger and more unusual structures. There is no detectable recent improvement in template-free modeling, but again, this may reflect the changing nature of CASP targets. © 2013 Wiley Periodicals, Inc.
引用
收藏
页码:164 / 174
页数:11
相关论文
共 20 条
[1]   Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].
Altschul, SF ;
Madden, TL ;
Schaffer, AA ;
Zhang, JH ;
Zhang, Z ;
Miller, W ;
Lipman, DJ .
NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402
[2]   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
[3]   Sequencing delivers diminishing returns for homology detection: implications for mapping the protein universe [J].
Chubb, Daniel ;
Jefferys, Benjamin R. ;
Sternberg, Michael J. E. ;
Kelley, Lawrence A. .
BIOINFORMATICS, 2010, 26 (21) :2664-2671
[4]   Emerging methods in protein co-evolution [J].
de Juan, David ;
Pazos, Florencio ;
Valencia, Alfonso .
NATURE REVIEWS GENETICS, 2013, 14 (04) :249-261
[5]   Assessment of template-based protein structure predictions in CASP10 [J].
Huang, Yuanpeng J. ;
Mao, Binchen ;
Aramini, James M. ;
Montelione, Gaetano T. .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2014, 82 :43-56
[6]   Sampling Bottlenecks in De novo Protein Structure Prediction [J].
Kim, David E. ;
Blum, Ben ;
Bradley, Philip ;
Baker, David .
JOURNAL OF MOLECULAR BIOLOGY, 2009, 393 (01) :249-260
[7]   CASP9 assessment of free modeling target predictions [J].
Kinch, Lisa ;
Shi, Shuo Yong ;
Cong, Qian ;
Cheng, Hua ;
Liao, Yuxing ;
Grishin, Nick V. .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2011, 79 :59-73
[8]   CASP9 target classification [J].
Kinch, Lisa N. ;
Shi, Shuoyong ;
Cheng, Hua ;
Cong, Qian ;
Pei, Jimin ;
Mariani, Valerio ;
Schwede, Torsten ;
Grishin, Nick V. .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2011, 79 :21-36
[9]   A GENERAL-METHOD FOR THE PREDICTION OF THE 3-DIMENSIONAL STRUCTURE AND FOLDING PATHWAY OF GLOBULAR-PROTEINS - APPLICATION TO DESIGNED HELICAL PROTEINS [J].
KOLINSKI, A ;
GODZIK, A ;
SKOLNICK, J .
JOURNAL OF CHEMICAL PHYSICS, 1993, 98 (09) :7420-7433
[10]   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