Functional classification of protein 3D structures from predicted local interaction sites

Journal of Bioinformatics and Computational Biology

Volumn 8, Issue SUPPL. 1, 2010, Pages 1-15

  Parasuram, Ramya ^a   Lee, Joslynn S ^a   Yin, Pengcheng ^a   Somarowthu, Srinivas ^a   Ondrechen, Mary Jo ^a  

^a NORTHEASTERN UNIVERSITY   (United States)

Author keywords

Functional annotation; POOL; structural genomics; THEMATICS

Indexed keywords

BACTEROIDES FRAGILIS; STREPTOMYCES COELICOLOR;

BACTERIAL PROTEIN; ENOYL COENZYME A HYDRATASE; EPIMERASE; GLUCAN 1,4 ALPHA GLUCOSIDASE; PROTEIN; PROTOZOAL PROTEIN; RIBULOSEPHOSPHATE 3 EPIMERASE; RIBULOSEPHOSPHATE 3-EPIMERASE;

ANIMAL; ARTICLE; ARTIFICIAL INTELLIGENCE; BACTEROIDES FRAGILIS; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; CLASSIFICATION; COMPUTER PROGRAM; ENZYME ACTIVE SITE; ENZYMOLOGY; PLASMODIUM FALCIPARUM; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEOMICS; STATIC ELECTRICITY; STATISTICS; STREPTOMYCES COELICOLOR; STRUCTURAL HOMOLOGY;

ANIMALS; ARTIFICIAL INTELLIGENCE; BACTERIAL PROTEINS; BACTEROIDES FRAGILIS; CARBOHYDRATE EPIMERASES; CATALYTIC DOMAIN; COMPUTATIONAL BIOLOGY; ENOYL-COA HYDRATASE; GLUCAN 1,4-ALPHA-GLUCOSIDASE; MODELS, MOLECULAR; PLASMODIUM FALCIPARUM; PROTEIN CONFORMATION; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEINS; PROTEOMICS; PROTOZOAN PROTEINS; SOFTWARE; STATIC ELECTRICITY; STREPTOMYCES COELICOLOR; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 78649986149     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720010005166     Document Type: Article

References (25)

1. Westbrook J, Feng Z, Chen L, Yang H, Berman HM, The protein data bank and structural genomics, Nucleic Acids Res 31:489-491, 2003. (Pubitemid 36150437)
2. Ondrechen MJ, Clifton JG, Ringe D, THEMATICS: A simple computational predictor of enzyme function from structure, Proc Natl Acad Sci USA 98:12473-12478, 2001. (Pubitemid 33019970)
3. Ko J, Murga LF, Andre P, Yang H, Ondrechen MJ, Williams RJ, Agunwamba A, Budil DE, Statistical criteria for the identification of protein active sites using theoretical microscopic titration curves, Proteins 59:183-195, 2005. (Pubitemid 40471558)
4. Wei Y, Ko J, Murga LF, Ondrechen MJ, Selective prediction of interaction sites in protein structures with THEMATICS, BMC Bioinformatics 8:119, 2007. (Pubitemid 47096945)
5. Tong W, Wei Y, Murga LF, Ondrechen MJ, Williams RJ, Partial Order Optimum Likelihood (POOL): Maximum likelihood prediction of protein active site residues using 3D structure and sequence properties, PLoS Comput Biol 5:e1000266, 2009.
6. Tong W, Williams RJ, Wei Y, Murga LF, Ko J, Ondrechen MJ, Enhanced performance in prediction of protein active sites with THEMATICS and support vector machines, Protein Sci 17:333-341, 2008. (Pubitemid 351171845)
7. Bartlett GJ, Porter CT, Borkakoti N, Thornton JM, Analysis of catalytic residues in enzyme active sites, J Mol Biol 324:105-121, 2002. (Pubitemid 35352183)
8. Ringe D, Wei Y, Boino KR, Ondrechen MJ, Protein structure to function: Insights from computation, Cell Mole Life Sci 61:387-392, 2004. (Pubitemid 38316577)
9. Murga LF, Ondrechen MJ, Ringe D, Prediction of interaction sites from apo 3D structures when the holo conformation is different, Proteins 72:980-992, 2008. (Pubitemid 352000875)
10. Chan CS, Winstone TML, Chang L, Li H, Stevens C, Workentine ML, Wei Y, Ondrechen MJ, Paetzel M, Turner RJ, Identification of a twin-arginine leader peptide binding site in DmsD; Defined through random and bioinformatics-directed mutage-nesis, Biochemistry 47:2749-2759, 2008. (Pubitemid 351328825)
11. Notredame C, Higgins DG, Heringa J, T-Coffee: A novel method for multiple sequence alignments, J Mol Biol 302:205-207, 2000.
12. Shindyalov IN, Bourne PE, Protein structure alignment by incremental combinatorial extension (CE) of the optimal path, Protein Eng 11:739-747, 1998.
13. Sankararaman S, Sjolander K, INTREPID: INformation-theoretic TREe traversal for Protein functional site IDentification, Bioinformatics 24:2445-2452, 2008.
14. Porter CT, Bartlett GJ, Thornton JM, The catalytic site atlas: A resource of catalytic sites and residues identified in enzymes using structural data, Nucleic Acids Res 32:D129-D133, 2004.
15. Holm L, Kaariainen S, Wilton C, Plewczynski D, Using dali for structural comparison of proteins, Curr Protoc Bioinformatics Chapter 5: Unit 5.5, 2006.
16. Murzin AG, Brenner SE, Hubbard T, Chothia C, SCOP: A structural classification of proteins database for the investigation of sequences and structures, J Mol Biol 247:536-540, 1995.
17. Brown SD, Gerlt JA, Seffernick JL, Babbitt PC, A gold standard set of mechanistically diverse enzyme superfamilies, Genome Biol 7:R8, 2006.
18. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ, Gapped BLAST and PSI-BLAST: A new generation of protein database search programs, Nucleic Acids Res 25:3389-3402, 1997. (Pubitemid 27359211)
19. Friedberg I, Harder T, Godzik A, JAFA: A protein function annotation meta-server, Nucleic Acids Res 34:W379-W381, 2006. (Pubitemid 44529797)
20. Zdobnov EM, Apweiler R, InterProScan - An integration platform for the signature-recognition methods in InterPro, Bioinformatics 17:847-848, 2001. (Pubitemid 32970486)
21. Glanville JG, Kirshner D, Krishnamurthy N, Sjolander K, Berkeley phylogenomics group web servers: Resources for structural phylogenomic analysis, Nucleic Acids Res 35:W27-W32, 2007.
22. Ilyin VA, Abyzov A, Leslin CM, Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point, Protein Sci 13:1865-1874, 2004.
23. Modis Y, Filppula SA, Novikov DK, Norledge B, Hiltunen JK, Wierenga RK, The crystal structure of dienoyl-CoA isomerase at 1.5 A resolution reveals the importance of aspartate and glutamate sidechains for catalysis, Structure 6:957-970, 1998. (Pubitemid 28397918)
24. Bahnson BJ, Anderson VE, Petsko GA, Structural mechanism of enoyl-CoA hydratase: Three atoms from a single water are added in either an E1cb stepwise or concerted fashion, Biochemistry 41:2621-2629, 2002.
25. Schnoes AM, Brown SD, Dodevski I, Babbitt PC, Annotation error in public databases: Misannotation of molecular function in enzyme superfamilies, PLoS Comput Biol 5:e1000605, 2009.