Identification of the ligand binding sites on the molecular surface of proteins

Protein Science

Volumn 14, Issue 3, 2005, Pages 711-718

  Kinoshita, Kengo ^a,b,c   Nakamura, Haruki ^a  

^a OSAKA UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

Author keywords

Hypothetical proteins; Protein three dimensional structure; Structural genomics; Structure based function prediction

Indexed keywords

ARTICLE; BINDING AFFINITY; BINDING SITE; COMPARATIVE STUDY; CONTROLLED STUDY; MATHEMATICAL ANALYSIS; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN TERTIARY STRUCTURE; STRUCTURAL GENOMICS; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS; THEORETICAL MODEL;

BINDING SITES; COMPUTER SIMULATION; DATABASES, PROTEIN; LIGANDS; MODELS, BIOLOGICAL; PROTEINS; S-ADENOSYLHOMOCYSTEINE;

EID: 14144254344     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.041080105     Document Type: Article

References (33)

1. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
2. Artymiuk, P.J., Poirrette, A.R., Grindley, H.M., Rice, D.W., and Willett, P. 1994. A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures. J. Mol. Biol. 243: 327-344.
3. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. 2000. The Protein Data Bank. Nucleic Acids Res. 28: 235-242.
4. Berman, H., Henrick, K., and Nakamura, H. 2003. Announcing the worldwide Protein Data Bank. Nat. Struct. Biol. 10: 980.
5. Brenner, S.E. 2001. A tour of structural genomics. Nat. Rev. Genet. 1: 801-809.
6. Brenner, S.E., Chothia, C., and Hubbard, T.J. 1997. Population statistics of protein structures: Lessons from structural classifications. Curr. Opin. Struct. Biol. 7: 369-376.
7. Connolly, M.L. 1983. Solvent-accessible surfaces of proteins and nucleic acids. Science 221: 709-713.
8. Dawe, J.H., Porter, C.T., Thornton, J.M., and Tabor, A.B. 2003. A template search reveals mechanistic similarities and differences in β-ketoacyl synthases (KAS) and related enzymes. Proteins 52: 427-435.
9. Durbin, R., Eddy, S., Krogh, A., and Mitchison, G. 1998. Biological sequence analysis: models of proteins and nucleic acids. Cambridge University Press, Cambridge, United Kingdom.
10. Handa, N., Terada, T., Kamewari, Y., Hamana, H., Tame, J.R., Park, S.Y., Kinoshita, K., Ota, M., Nakamura, H., Kuramitsu, S., et al. 2003. Crystal structure of the conserved protein TT1542 from Thermus thermophilus HB8. Protein Sci. 12: 1621-1632.
11. Higgins, D.G., Thompson, J.D., and Gibson, T.J. 1996. Using CLUSTAL for multiple sequence alignments. Methods Enzymol. 266: 393-402.
12. Holm, L. and Park, J. 2000. DaliLite workbench for protein structure comparison. Bioinformatics 16: 566-567.
13. Holm, L. and Sander, C. 1996. Mapping the protein universe. Science 273: 595-603.
14. Kinoshita, K., and Nakamura, H. 2003. Identification of protein biochemical functions by similarity search using the molecular surface database eF-site. Protein Sci. 12: 1589-1595.
15. _. 2004. eF-site and PDBjViewer: database and viewer for protein functional sites. Bioinformatics 20: 1329-1330.
16. Kinoshita, K., Sadanami, K., Kidera, A., and Go, N. 1999. Structural motif of phosphate-binding site common to various protein superfamilies: All-against-all structural comparison of protein-mononucleotide complexes. Protein Eng. 12: 11-14.
17. Kinoshita, K., Furui, J., and Nakamura, H. 2002. Identification of protein functions from a molecular surface database, eF-site. J. Struct. Funct. Genomics 2: 9-22.
18. Kleywegt, G.J. 1999. Recognition of spatial motifs in protein structures. J. Mol. Biol. 285: 1887-1897.
19. Kraulis, P.J. 1991. MOLSCRIPT: A program to produce both detailed and schematic plots of proteins structures. J. Appl. Cryst. 24: 946-950.
20. Lim, K., Zhang, H., Tempczyk, A., Krajewski, W., Bonander, N., Toedt, J., Howard, A., Eisenstein, E., and Herzberg, O. 2003. Structure of the YibK methyltransferase from Haemophilus influenzae (HI0766 (IJ85)): A cofactor bound at a site formed by a knot. Proteins 51: 56-67.
21. Lin, S.L. and Nussinov, R. 1996. Molecular recognition via face center representation of a molecular surface. J. Mol. Graph. 14: 78-90, 95-77.
22. Lin, S.L., Nussinov, R., Fischer, D., and Wolfson, H.J. 1994. Molecular surface representations by sparse critical points. Proteins 18: 94-101.
23. Lo Conte, L., Brenner, S.E., Hubbard, T.J., Chothia, C., and Murzin, A.G. 2002. SCOP database in 2002: Refinements accommodate structural genomics. Nucleic Acids Res. 30: 264-267.
24. Mihalek, I., Res, I., and Lichtarge, O. 2004. A family of evolution-entropy hybrid methods for ranking protein residues by importance. J. Mol. Biol. 336: 1265-1282.
25. Moodie, S.L., Mitchell, J.B., and Thornton, J.M. 1996. Protein recognition of adenylate: An example of a fuzzy recognition template. J. Mol. Biol. 263: 486-500.
26. Orengo, C.A., Jones, D.T., and Thornton, J.M. 1994. Protein superfamilies and domain superfolds. Nature 372: 631-634.
27. Pearson, W.R. 1994. Using the FASTA program to search protein and DNA sequence databases. Methods Mol. Biol. 24: 307-331.
28. Rosen, M., Lin, S.L., Wolfson, H., and Nussinov, R. 1998. Molecular shape comparisons in searches for active sites and functional similarity. Protein Eng. 11: 263-277.
29. Shulman-Peleg, A., Nussinov, R., and Wolfson, H.J. 2004. Recognition of functional sites in protein structures. J. Mol. Biol. 339: 607-633.
30. Thornton, J.M., Todd, A.E., Milburn, D., Borkakoti, N., and Orengo, C.A. 2000. From structure to function: Approaches and limitations. Nat. Struct. Biol. 7(Suppl): 991-994.
31. Todd, A.E., Orengo, C.A., and Thornton, J.M. 2001. Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol. 307: 1113-1143.
32. Wallace, A.C., Laskowski, R.A., and Thornton, J.M. 1996. Derivation of 3D coordinate templates for searching structural databases: Application to Ser-His-Asp catalytic triads in the serine proteinases and lipases. Protein Sci. 5: 1001-1013.
33. Wallace, A.C., Borkakoti, N., and Thornton, J.M. 1997. TESS: A geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases: Application to enzyme active sites. Protein Sci. 6: 2308-2323.