A protein sequence meta-functional signature for calcium binding residue prediction

Pattern Recognition Letters

Volumn 31, Issue 14, 2010, Pages 2103-2112

  Horst, Jeremy A ^a   Samudrala, Ram ^b  

^a UNIVERSITY OF WASHINGTON   (United States)

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

Author keywords

Calcium; Functional signature; Protein binding site; Protein function prediction; Protein sequence analysis

Indexed keywords

ADDED VALUES; AMINO ACID RESIDUES; CALCIUM BINDING; CALCIUM IONS; CHEMICAL MOIETIES; CROSS VALIDATION; FUNCTIONAL INTERACTION; FUNCTIONAL SIGNATURES; GENERALIZED FUNCTIONS; GEOMETRIC DISTRIBUTION; PARALLEL SETS; PREDICTIVE ABILITIES; PROTEIN BINDING SITE; PROTEIN FUNCTION PREDICTION; PROTEIN FUNCTIONS; PROTEIN SEQUENCE ANALYSIS; PROTEIN SEQUENCES; RECEIVER OPERATOR CHARACTERISTIC CURVES; RESIDUE FUNCTIONS; SECONDARY STRUCTURES; SIDE CHAINS; SPATIAL RELATIONS; STRUCTURAL FEATURE; TERTIARY STRUCTURES;

AMINO ACIDS; BINDING ENERGY; BINDING SITES; BIOCHEMISTRY; CALCIUM; FORECASTING; KNOWLEDGE BASED SYSTEMS; MATHEMATICAL OPERATORS; ORGANIC ACIDS; PERSONNEL TRAINING;

PROTEINS;

EID: 77956341043     PISSN: 01678655     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.patrec.2010.04.012     Document Type: Article

References (45)

1. R. Abagyan, and I. Kufareva The flexible pocketome engine for structural chemogenomics Methods Mol. Biol. 575 2009 249 279
2. S.F. Altschul, T.L. Madden, A.A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic Acids Res. 25 1997 3389 3402
3. J. Ashworth, J.J. Havranek, C.M. Duarte, D. Sussman, R.J. Monnat, B.L. Stoddard, and D. Baker Computational redesign of endonuclease DNA binding and cleavage specificity Nature 441 2006 656 659
4. H. Berman, K. Henrick, H. Nakamura, and J.L. Markley The worldwide Protein Data Bank (wwPDB): Ensuring a single, uniform archive of PDB data Nucleic Acids Res. 35 2007 D301 D303
5. A. Biegert, and J. Söding Sequence context-specific profiles for homology searching Proc. Natl. Acad. Sci. USA 106 2009 3770 3775
6. P. Bork, T. Dandekar, Y. Diaz-Lazcoz, F. Eisenhaber, M. Huynen, and Y. Yuan Predicting function: From genes to genomes and back J. Mol. Biol. 283 1998 707 725
7. L. Chen, R. Oughtred, H.B. Berman, and J. Westbrook TargetDB: A target registration database for structural genomics projects Bioinformatics 20 2004 2860 2862
8. G. Cheng, B. Qian, R. Samudrala, and D. Baker Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design Nucleic Acids Res. 33 2005 5861 5867
9. H. Deng, G. Chen, W. Yang, and J.J. Yang Predicting calcium-binding sites in proteins - A graph theory and geometry approach Proteins 64 2006 34 42
10. S.R. Eddy Profile hidden Markov models Bioinformatics 14 1998 755 763
11. R.C. Edgar MUSCLE: Multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res. 32 2004 1792 1797
12. J. Felsenstein Evolutionary trees from DNA sequences: A maximum likelihood approach J. Mol. Evol. 17 1981 368 376
13. J.S. Fetrow, and J. Skolnick Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases J. Mol. Biol. 281 1998 949 968
14. J.D. Fischer, C.E. Mayer, and J. Söding Prediction of protein functional residues from sequence by probability density estimation Bioinformatics 24 2008 613 620
15. K. Fleming, L.A. Kelley, S.A. Islam, R.M. MacCallum, A. Muller, F. Pazos, and M.J. Sternberg The proteome: Structure, function and evolution Philos. Trans. Roy. Soc. Lond. B - Biol. Sci. 29 2006 441 451
16. H. Ge, A.J. Walhout, and M. Vidal Integrating 'omic' information: A bridge between genomics and systems biology Trends Genet. 19 2003 551 560
17. A. Gutteridge, and J.M. Thornton Understanding nature's catalytic toolkit Trends Biochem. Sci. 30 2005 622 629
18. Horst, J.A., Samudrala, R., 2009. Diversity of protein structures and difficulties in fold recognition: The curious case of protein G. F1000 Biology Reports, vol. 1, p. 69.
19. R.A. Jensen Enzyme recruitment in evolution of new function Annu. Rev. Microbiol. 30 1974 409 425
20. L. Jiang, E.A. Althoff, F.R. Clemente, L. Doyle, D. Röthlisberger, A. Zanghellini, J.L. Gallaher, J.L. Betker, F. Tanaka, C.F. Barbas, D. Hilvert, K.N. Houk, B.L. Stoddard, and D. Baker De novo computational design of retro-aldol enzymes Science 319 2008 1387 1391
21. D.T. Jones Protein secondary structure prediction based on position-specific scoring matrices J. Mol. Biol. 292 1999 195 202
22. O. Khersonsky, C. Roodveldt, and D.S. Tawfik Enzyme promiscuity: Evolutionary and mechanistic aspects Curr. Opin. Chem. Biol. 10 2006 498 508
23. R.A. Laskowski, J.D. Watson, and J.M. Thornton Protein function prediction using local 3D templates J. Mol. Biol. 351 2005 614 626
24. N.K. Lee, H. Sowa, E. Hinoi, M. Ferron, and J.D. Ahn Endocrine regulation of energy metabolism by the skeleton Cell 130 2007 456 469
25. G. Lopez, I. Ezkurdia, and M.L. Tress Assessment of ligand binding residue predictions in CASP8 Proteins 77 Suppl. 9 2009 138 146
26. M. Margelevicius, and C. Venclovas PSI-BLAST-ISS: An intermediate sequence search tool for estimation of the position-specific alignment reliability BMC Bioinform. 6 2005 185
27. J. McDermott, R.E. Bumgarner, and R. Samudrala Functional annotation from predicted protein interaction networks Bioinformatics 21 2005 3217 3226
28. I. Mihalek, I. Res, and O. Lichtarge A family of evolution - Entropy hybrid methods for ranking protein residues by importance J. Mol. Biol. 336 2004 1265 1282
29. J. Moult A decade of CASP: Progress, bottlenecks and prognosis in protein structure prediction Curr. Opin. Struct. Biol. 15 2005 285 289
30. D.H. O'Day CaMBOT: Profiling and characterizing calmodulin-binding proteins Cell. Signal. 15 2003 347 354
31. Protein Data Bank. Research Collaboratory for Structural Bioinformatics. < http://www.pdb.org > (accessed 17.07.09).
32. Protein Structure Initiative. Structural Genomics Knowledgebase: TargetDB Statistics Summary Report. < http://targetdb.pdb.org/statistics/ TargetStatistics.html > (accessed 11.11.09).
33. K.D. Pruitt, T. Tatusova, and D.R. Maglott NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins Nucl Acids Res. 33 2005 D501 D504
34. S. Raman, R. Vernon, J. Thompson, M. Tyka, R. Sadreyev, J. Pei, D. Kim, E. Kellogg, F. DiMaio, O. Lange, L. Kinch, W. Sheffler, B.H. Kim, R. Das, N.V. Grishin, and D. Baker Structure prediction for CASP8 with all-atom refinement using Rosetta Proteins 77 Suppl. 9 2009 89 99
35. G.A. Reeves, D. Talavera, and J.M. Thornton Genome and proteome annotation: Organization, interpretation and integration J. Roy. Soc. Interface 6 2009 129 147
36. B.A. Shoemaker, J.J. Portman, and P.G. Wolynes Speeding molecular recognition by using the folding funnel: The fly-casting mechanism Proc. Natl. Acad. Sci. USA 97 2000 8868 8873
37. B. Sterner, R. Singh, and B. Berger Predicting and annotating catalytic residues: An information theoretic approach J. Comput. Biol. 14 2007 1058 1073
38. E.A. Stone, and A. Sidow Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity Genome Res. 15 2005 978 986
39. M.G. Tordoff Calcium: Taste, intake, and appetite Physiol. Rev. 81 2001 1567 1597
40. US Department of Energy Joint Genome Institute: Intergrated Microbial Genomes. < http://img.jgi.doe.gov > (accessed 18.11.09).
41. K. Wang, and R. Samudrala Incorporating background frequency improves entropy-based residue conservation measures BMC Bioinform. 7 2006 385
42. K. Wang, J.A. Horst, G. Cheng, D. Nickle, and R. Samudrala Protein meta-functional signatures from combining sequence, structure, evolution and amino acid property information PLoS Comput. Biol. 4 2008 e1000181
43. 2+-binding sites with different coordination numbers in proteins with atomic resolution Proteins 75 2009 787 798
44. Y. Zhang Progress and challenges in protein structure prediction Curr. Opin. Struct. Biol. 18 2008 342 348
45. T. Zhang, H. Zhang, K. Chen, S. Shen, J. Ruan, and L. Kurgan Accurate sequence-based prediction of catalytic residues Bioinformatics 24 2008 2329 2338