Direct correlation analysis improves fold recognition

Computational Biology and Chemistry

Volumn 35, Issue 5, 2011, Pages 323-332

  Sadowski, Michael I ^a   Maksimiak, Katarzyna ^a   Taylor, William R ^a  

^a NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

Author keywords

Decoy models; Direct information; Protein fold recognition

Indexed keywords

BETA-SHEET; CORRELATION ANALYSIS; DECOY MODELS; DIRECT INFORMATION; FOLD RECOGNITION; PROTEIN FOLD RECOGNITION; PROTEIN FOLDS; THREE-DIMENSIONAL STRUCTURE;

PROTEIN FOLDING;

PROTEINS;

PROTEIN;

ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; PROTEIN CONFORMATION; PROTEIN DATABASE; PROTEIN FOLDING;

COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS;

EID: 80052852201     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2011.08.002     Document Type: Article

References (30)

1. D. Altschuh, A.M. Lesk, A.C. Bloomer, and A. Klug Correlation of coordinated amino-acid substitutions with function in tobamoviruses Protein Eng. 1 1987 228
2. S.F. Altschul, T.L. Madden, A.A. Schäffer, J.H. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucl. Acid Res. 25 1997 3389 3402 (Pubitemid 27359211)
3. A. Aszódi, M.J. Gradwell, and W.R. Taylor Global fold determination from a small number of distance restraints J. Mol. Biol. 251 1995 308 326
4. A. Aszódi, and W.R. Taylor Secondary structure formation in model polypeptide chains Protein Eng. 7 1994 633 644 (Pubitemid 24150072)
5. A. Aszódi, and W.R. Taylor Estimating polypeptide α-carbon distances from multiple sequence alignments J. Math. Chem. 17 1995 167 184
6. G.J. Bartlett, and W.R. Taylor Using scores derived from statistical coupling analysis to distinguish correct and incorrect folds in de-novo protein structure prediction Proteins: Struct. Funct. Bioinfo. 71 2007 950 959 (Pubitemid 351430027)
7. L. Burger, and E. van Nimwegen Disentangling direct from indirect co-evolution of residues in protein alignments PLoS Comp. Biol. 6 2010 1 17
8. U. Gobel, C. Sander, R. Schneider, and A. Valencia Correlated mutations and residue contacts in proteins Protein Struct. Funct. Genet. 18 1994 309 317 (Pubitemid 24111530)
9. K. Hatrick, and W.R. Taylor Sequence conservation and correlation measures in protein structure prediction Comput. Chem. 18 1994 245 250
10. S.M. Hollup, M.I. Sadowski, I. Jonassen, and W.R. Taylor Exploring the limits of fold discrimination by structural alignment: a large scale benchmark using decoys of known fold Comput. Biol. Chem. 35 2011 174 188
11. D.T. Jones Protein secondary structure prediction based on position-specific scoring matrices J. Mol. Biol. 292 1999 195 202 (Pubitemid 29435759)
12. D.T. Jones The PSIPRED protein structure prediction server Bioinformatics 16 2000 404 405 (Pubitemid 30417087)
13. A.S. Lapedes, B.G. Giraud, L. Liu, and G.D. Stormo Stat. Mol. Biol. 33 1999 236 256
14. K. Lin, V.A. Simossis, W.R. Taylor, and J. Heringa A simple and fast secondary structure prediction method using hidden neural networks Bioinformatics 21 2005 152 159 (Pubitemid 40202016)
15. S.W. Lockless, and R. Ranganathan Evolutionarily conserved pathways of energetic connectivity in protein families Science 286 5438 1999 295 299 (Pubitemid 29484693)
16. J.T. MacDonald, K. Maksimiak, M.I. Sadowski, and W.R. Taylor de novo backbone scaffolds for protein design Protein Struct. Funct. Bioinf. 78 2009 1311 1325
17. E. Neher How frequent are correlated changes in families of protein sequences? Proc. Natl. Acad. Sci. U.S.A. 91 1994 98 102 (Pubitemid 24018650)
18. D.D. Pollock, and W.R. Taylor Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution Protein Eng. 10 1997 647 657 (Pubitemid 27332071)
19. D.D. Pollock, W.R. Taylor, and N. Goldman Coevolving protein residues: maximum likelihood identification and relationship to structure J. Mol. Biol. 287 1999 187 198 (Pubitemid 29134806)
20. M.S. Singer, G. vriend, and R.P. Bywater Prediction of protein residue contacts with a PDB-derived likelihood matrix Protein Eng. 15 2002 721 725 (Pubitemid 35470428)
21. M. Socolich, S.W. Lockless, W.P. Russ, H. Lee, K.H. Gardner, and R. Ranganathan Evolutionary information for specifying a protein fold Nature 437 7058 2005 512 518 (Pubitemid 41613543)
22. G.M. Suel, S.W. Lockless, M.A. Wall, and R. Ranganathan Evolutionarily conserved networks of residues mediate allosteric communication in proteins Nat. Struct. Biol. 10 1 2003 59 69 (Pubitemid 36034178)
23. W.R. Taylor A periodic table for protein structure Nature 416 2002 657 660
24. W.R. Taylor, G.J. Bartlett, V. Chelliah, D. Klose, K. Lin, T. Sheldon, and I. Jonassen Prediction of protein structure from ideal forms Proteins: Struct. Funct. Bioinfo. 70 2008 1610 1619 (Pubitemid 351304117)
25. W.R. Taylor, S.M. Hollup, J.T. MacDonnald, and I. Jonassen Probing the "dark matter" of protein fold-space Structure 17 2009 1244 1252
26. W.R. Taylor, K. Lin, D. Klose, F. Fraternali, and I. Jonassen Dynamic domain threading Proteins Struct. Funct. Bioinfo. 64 2006 601 614 (Pubitemid 44100727)
27. A. Valencia, and F. Pazos Computational methods for the prediction of protein interactions Curr. Opin. Struct. Biol. 12 2002 368 373 (Pubitemid 34804620)
28. B. Wang, P. Chen, D. Huang, J. Li, T. Lok, and M. Lyu Predicting protein interaction sites from residue spatial sequence profile and evolution rate FEBS Lett. 580 2006 380 384 (Pubitemid 43089660)
29. Weigt, M.; 2011. Interprotein residue contacts and interaction specificity in bacterial signal transduction. KITP online archives. http://online.kitp.ucsb.edu/online/viral11/weigt (slide 13).
30. M. Weigt, R.A. White, H. Szurmantc, J.A. Hochc, and T. Hwa Identification of direct residue contacts in protein/protein interaction by message passing PNAS 106 2009 67 72