Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era

Proceedings of the National Academy of Sciences of the United States of America

Volumn 110, Issue 39, 2013, Pages 15674-15679

  Kamisetty, Hetunandan ^a,b   Ovchinnikov, Sergey ^a,b   Baker, David ^a,b  

^a UNIVERSITY OF WASHINGTON   (United States)

^b UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

Author keywords

Markov random field; Maximum entropy model; Protein coevolution

Indexed keywords

AMINO ACID; PROTEIN;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; COEVOLUTION; PREDICTION; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN STRUCTURE;

MARKOV RANDOM FIELD; MAXIMUM-ENTROPY MODEL; PROTEIN COEVOLUTION;

ALGORITHMS; AMINO ACID SEQUENCE; AMINO ACIDS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; EVOLUTION, MOLECULAR; MODELS, MOLECULAR; PROTEINS;

EID: 84884603324     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1314045110     Document Type: Article

References (24)

1. Tress ML, Valencia A (2010) Predicted residue-residue contacts can help the scoring of 3d models. Proteins. Struct Funct Bioinf 78(8):1980-1991.
2. Morcos F, et al. (2011) Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci USA 108(49):E1293-E1301.
3. Jones DT, Buchan DWA, Cozzetto D, Pontil M (2012) PSICOV: Precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics 28(2):184-190.
4. Marks DS, et al. (2011) Protein 3D structure computed from evolutionary sequence variation. PLoS ONE 6(12):e28766.
5. Balakrishnan S, Kamisetty H, Carbonell JG, Lee SI, Langmead CJ (2011) Learning generative models for protein fold families. Protiens Struct Funct Bioinf 79(4):1061-1078.
6. Ekeberg M, Lövkvist C, Lan Y, Weigt M, Aurell E (2013) Improved contact prediction in proteins: using pseudolikelihoods to infer Potts models. Phys Rev E Stat Nonlin Soft Matter Phys 87(1):012707.
7. Arnold K, et al. (2009) The protein model portal. J Struct Funct Genomics 10(1):1-8.
8. Dunn SD, Wahl LM, Gloor GB (2008) Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction. Bioinformatics 24(3):333-340.
9. McGuffin LJ, Bryson K, Jones DT (2000) The PSIPRED protein structure prediction server. Bioinformatics 16(4):404-405.
10. Cheng J, Baldi P (2007) Improved residue contact prediction using support vector machines and a large feature set. BMC Bioinf 8(1):113.
11. Su?kowska JI, Morcos F, Weigt M, Hwa T, Onuchic JN (2012) Genomics-aided structure prediction. Proc Natl Acad Sci USA 109(26):10340-10345.
12. Nugent T, Jones DT (2012) Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis. Proc Natl Acad Sci USA 109(24):E1540-E1547.
13. Berman HM, et al. (2000) The protein data bank. Nucleic Acids Res 28(1):235-242.
14. Zhang Y, Skolnick J (2005) TM-align: A protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 33(7):2302-2309.
15. Hopf TA, et al. (2012) Three-dimensional structures of membrane proteins from genomic sequencing. Cell 149(7):1607-1621.
16. Weigt M, White RA, Szurmant H, Hoch JA, Hwa T (2009) Identification of direct residue contacts in protein-protein interaction by message passing. Proc Natl Acad Sci USA 106(1):67-72.
17. Thomas J, Ramakrishnan N, Bailey-Kellogg C (2008) Graphical models of residue coupling in protein families. IEEE/ACM Trans Comp Bio Bioinf 5(2):183-197.
18. Banerjee O, El Ghaoui L, d'Aspremont A (2008) Model selection through sparse maximum likelihood estimation for multivariate Gaussian or binary data. J Mach Learn Res 9:485-516.
19. Gidas B (1988) Consistency of maximum likelihood and pseudo-likelihood estimators for Gibbs distributions. J Inst Math Its Appl 10:129-145.
20. Söding J (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21(7):951-960.
21. Bateman A, et al. (2002) The PFAM protein families database. Nucleic Acids Res 30(1): 276-280.
22. Biegert A, Mayer C, Remmert M, Söding J, Lupas AN (2006) The MPI Bioinformatics Toolkit for protein sequence analysis. Nucleic Acids Res 34(Web Server issue, Suppl 2): W335-9.
23. Wang G, Dunbrack RL, Jr. (2005) PISCES: Recent improvements to a PDB sequence culling server. Nucleic Acids Res 33(Web Server issue, Suppl 2):W94-8.
24. Jeong CS, Kim D (2012) Reliable and robust detection of coevolving protein residues. Protein Engineering Design and Selection, 25(11):705-713.