PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

被引：566

作者：

Jones, David T. ^{[1
]}

Buchan, Daniel W. A. ^{[1
]}

Cozzetto, Domenico ^{[1
]}

Pontil, Massimiliano ^{[2
]}

机构：

[1] UCL, Dept Comp Sci, Bioinformat Grp, London WC1E 6BT, England

[2] UCL, Dept Comp Sci, Ctr Computat Stat & Machine Learning, London WC1E 6BT, England

来源：

BIOINFORMATICS | 2012年 / 28卷 / 02期

基金：

英国生物技术与生命科学研究理事会; 英国工程与自然科学研究理事会;

关键词：

RESIDUE CONTACTS; CORRELATED MUTATIONS; PROTEIN; IDENTIFICATION; INFORMATION; PHYLOGENY; SELECTION; FAMILIES; IMPROVES; NUMBER;

D O I：

10.1093/bioinformatics/btr638

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Results: PSICOV displays a mean precision substantially better than the best performing normalized mutual information approach and Bayesian networks. For 118 out of 150 targets, the L/5 (i.e. top-L/5 predictions for a protein of length L) precision for long-range contacts (sequence separation > 23) was >= 0.5, which represents an improvement sufficient to be of significant benefit in protein structure prediction or model quality assessment.

引用

页码：184 / 190

页数：7

共 42 条

[1] Reducing phylogenetic bias in correlated mutation analysis [J].

Ashkenazy, Haim ;

Kliger, Yossef .

PROTEIN ENGINEERING DESIGN & SELECTION, 2010, 23 (05) :321-326

[2]

Banerjee O, 2008, J MACH LEARN RES, V9, P485

[3] The Protein Data Bank [J].

Berman, HM ;

Westbrook, J ;

Feng, Z ;

Gilliland, G ;

Bhat, TN ;

Weissig, H ;

Shindyalov, IN ;

Bourne, PE .

NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :235-242

[4]

Bühlmann P, 2011, SPRINGER SER STAT, P1, DOI 10.1007/978-3-642-20192-9

[5] Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments [J].

Burger, Lukas ;

van Nimwegen, Erik .

PLOS COMPUTATIONAL BIOLOGY, 2010, 6 (01)

[6] Is There an Optimal Substitution Matrix for Contact Prediction with Correlated Mutations? [J].

Di Lena, Pietro ;

Fariselli, Piero ;

Margara, Luciano ;

Vassura, Marco ;

Casadio, Rita .

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2011, 8 (04) :1017-1028

[7] Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction [J].

Dunn, S. D. ;

Wahl, L. M. ;

Gloor, G. B. .

BIOINFORMATICS, 2008, 24 (03) :333-340

[8] 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

[9] Prediction of contact maps with neural networks and correlated mutations [J].

Fariselli, P ;

Olmea, O ;

Valencia, A ;

Casadio, R .

PROTEIN ENGINEERING, 2001, 14 (11) :835-843

[10] The Pfam protein families database [J].

Finn, Robert D. ;

Mistry, Jaina ;

Tate, John ;

Coggill, Penny ;

Heger, Andreas ;

Pollington, Joanne E. ;

Gavin, O. Luke ;

Gunasekaran, Prasad ;

Ceric, Goran ;

Forslund, Kristoffer ;

Holm, Liisa ;

Sonnhammer, Erik L. L. ;

Eddy, Sean R. ;

Bateman, Alex .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D211-D222

← 1 2 3 4 5 →