Predicting protein contact map using evolutionary and physical constraints by integer programming

Bioinformatics

Volumn 29, Issue 13, 2013, Pages

  Wang, Zhiyong ^a   Xu, Jinbo ^a  

^a TOYOTA TECHNOLOGICAL INSTITUTE AT CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ARTIFICIAL INTELLIGENCE; CHEMISTRY; MOLECULAR EVOLUTION; PROTEIN SECONDARY STRUCTURE; SEQUENCE HOMOLOGY; SYSTEM ANALYSIS; ARTICLE;

ARTIFICIAL INTELLIGENCE; EVOLUTION, MOLECULAR; PROGRAMMING, LINEAR; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 84879976691     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt211     Document Type: Conference Paper

References (33)

1. Altschul, S.F. and Koonin, E.V. (1998) Iterated profile searches with PSI-BLAST - A tool for discovery in protein databases. Trends Biochem. Sci., 23, 444-447.
2. Baú, D. et al. (2006) Distill: A suite of web servers for the prediction of one-, two-and three-dimensional structural features of proteins. BMC Bioinformatics, 7, 402.
3. Breiman, L. (2001) Random forests. Mach. Learn., 45, 5-32.
4. Brenner, S.E. et al. (2000) The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res., 28, 254-256.
5. Caprara, A. et al. (2004) 1001 optimal PDB structure alignments: Integer programming methods for finding the maximum contact map overlap. J. Comput. Biol., 11, 27-52.
6. Cheng, J. and Baldi, P. (2007) Improved residue contact prediction using support vector machines and a large feature set. BMC Bioinformatics, 8, 113.
7. International Business Machines Corporation (2009) IBM ILOG CPLEX. V12. 1: User's Manual for
8. CPLEX. Di Lena, P. et al. (2012) Deep architectures for protein contact map prediction. Bioinformatics, 28, 2449-2457.
9. Fariselli, P. and Casadio, R. (1999) A neural network based predictor of residue contacts in proteins. Protein Eng., 12, 15-21.
10. Göbel, U. et al. (2004) Correlated mutations and residue contacts in proteins. Proteins, 18, 309-317.
11. Jones, D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 292, 195-202.
12. Jones, D.T. et al. (2012) PSICOV: Precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics, 28, 184-190.
13. Klepeis, J. and Floudas, C. (2003) ASTRO-FOLD: A combinatorial and global optimization framework for ab initio prediction of three-dimensional structures of proteins from the amino acid sequence. Biophys. J., 85, 2119-2146.
14. Li, W. and Godzik, A. (2006) Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658-1659.
15. Li, W. et al. (2001) Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics, 17, 282-283.
16. Liaw, A. and Wiener, M. (2002) Classification and regression by randomforest. R News, 2, 18-22.
17. Morcos, F. et al. (2011) Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc. Natl. Acad. Sci. USA, 108, E1293-E1301.
18. Olmea, O. and Valencia, A. (1997) Improving contact predictions by the combination of correlated mutations and other sources of sequence information. Fold. Des., 2, S25-S32.
19. Ortiz, A.R. et al. (1999) Ab initio folding of proteins using restraints derived from evolutionary information. Proteins, 37, 177-185.
20. Punta, M. and Rost, B. (2005) PROFcon: Novel prediction of long-range contacts. Bioinformatics, 21, 2960-2968.
21. Tan, Y.H. et al. (2006) Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences. Proteins, 64, 587-600.
22. Tegge, A.N. et al. (2009) NNcon: Improved protein contact map prediction using 2D-recursive neural networks. Nucleic Acids Res., 37, W515-W518.
23. Vassura, M. et al. (2008) Reconstruction of 3D structures from protein contact maps. IEEE/ACM Trans. Comput. Biol. Bioinform., 5, 357-367.
24. Vendruscolo, M. and Domany, E. (1998) Pairwise contact potentials are unsuitable for protein folding. J. Chem. Phys., 109, 11101.
25. Vendruscolo, M. et al. (1997) Recovery of protein structure from contact maps. Fold. Des., 2, 295-306.
26. Vullo, A. et al. (2006) A two-stage approach for improved prediction of residue contact maps. BMC Bioinformatics, 7, 180.
27. Wang, G. and Dunbrack, R.L., Jr. (2003) PISCES: A protein sequence culling server. Bioinformatics, 19, 1589-1591.
28. Wang, S. et al. (2013) Protein structure alignment beyond spatial proximity. Sci. Rep., 3, 1448.
29. Wu, S. et al. (2011) Improving protein structure prediction using multiple sequencebased contact predictions. Structure, 19, 1182-1191.
30. Wu, S. and Zhang, Y. (2008) A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. Bioinformatics, 24, 924-931.
31. Xu, J. et al. (2007) A parameterized algorithm for protein structure alignment. J. Comput. Biol., 14, 564-577.
32. Zhao, F. and Xu, J. (2012) A position-specific distance-dependent statistical potential for protein structure and functional study. Structure, 20, 1118-1126.
33. Zhou, H. and Skolnick, J. (2007) Protein model quality assessment prediction by combining fragment comparisons and a consensus Cα contact potential. Proteins, 71, 1211-1218.