A conformation ensemble approach to protein residue-residue contact

被引:15
作者
Eickholt, Jesse [1 ]
Wang, Zheng [1 ]
Cheng, Jianlin [1 ,2 ,3 ]
机构
[1] Univ Missouri, Dept Comp Sci, Columbia, MO 65211 USA
[2] Univ Missouri, Inst Informat, Columbia, MO 65211 USA
[3] Univ Missouri, C Bond Life Sci Ctr, Columbia, MO 65211 USA
关键词
CORRELATED MUTATIONS; PREDICTION; QUALITY;
D O I
10.1186/1472-6807-11-38
中图分类号
Q6 [生物物理学];
学科分类号
071011 ;
摘要
Background: Protein residue-residue contact prediction is important for protein model generation and model evaluation. Here we develop a conformation ensemble approach to improve residue-residue contact prediction. We collect a number of structural models stemming from a variety of methods and implementations. The various models capture slightly different conformations and contain complementary information which can be pooled together to capture recurrent, and therefore more likely, residue-residue contacts. Results: We applied our conformation ensemble approach to free modeling targets from both CASP8 and CASP9. Given a diverse ensemble of models, the method is able to achieve accuracies of. 48 for the top L/5 medium range contacts and. 36 for the top L/5 long range contacts for CASP8 targets (L being the target domain length). When applied to targets from CASP9, the accuracies of the top L/5 medium and long range contact predictions were. 34 and. 30 respectively. Conclusions: When operating on a moderately diverse ensemble of models, the conformation ensemble approach is an effective means to identify medium and long range residue-residue contacts. An immediate benefit of the method is that when tied with a scoring scheme, it can be used to successfully rank models.
引用
收藏
页数:8
相关论文
共 36 条
[1]   Hidden conformations in protein structures [J].
Ashkenazy, Haim ;
Unger, Ron ;
Kliger, Yossef .
BIOINFORMATICS, 2011, 27 (14) :1941-1947
[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]   Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts [J].
Bjorkholm, Patrik ;
Daniluk, Pawel ;
Kryshtafovych, Andriy ;
Fidelis, Krzysztof ;
Andersson, Robin ;
Hvidsten, Torgeir R. .
BIOINFORMATICS, 2009, 25 (10) :1264-1270
[4]   Toward high-resolution de novo structure prediction for small proteins [J].
Bradley, P ;
Misura, KMS ;
Baker, D .
SCIENCE, 2005, 309 (5742) :1868-1871
[5]   Improved residue contact prediction using support vector machines and a large feature set [J].
Cheng, Jianlin ;
Baldi, Pierre .
BMC BIOINFORMATICS, 2007, 8 (1)
[6]   Evaluation of CASP8 model quality predictions [J].
Cozzetto, Domenico ;
Kryshtafovych, Andriy ;
Tramontano, Anna .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2009, 77 :157-166
[7]   Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8 [J].
Ezkurdia, Iakes ;
Grana, Osvaldo ;
Izarzugaza, Jose M. G. ;
Tress, Michael L. .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2009, 77 :196-209
[8]   Influence of conservation on calculations of amino acid covariance in multiple sequence alignments [J].
Fodor, AA ;
Aldrich, RW .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2004, 56 (02) :211-221
[9]   CORRELATED MUTATIONS AND RESIDUE CONTACTS IN PROTEINS [J].
GOBEL, U ;
SANDER, C ;
SCHNEIDER, R ;
VALENCIA, A .
PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1994, 18 (04) :309-317
[10]   CASP6 assessment of contact prediction [J].
Graña, O ;
Baker, D ;
MacCallum, RM ;
Meiler, J ;
Punta, M ;
Rost, B ;
Tress, ML ;
Valencia, A .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2005, 61 :214-224