Chemocavity: Specific concavity in protein reserved for the binding of biologically functional small molecules

Journal of Chemical Information and Modeling

Volumn 48, Issue 8, 2008, Pages 1679-1685

  Soga, Shinji ^a   Shirai, Hiroki ^a   Kobori, Masato ^a   Hirayama, Noriaki ^b  

^a ASTELLAS PHARMA INC   (Japan)

^b TOKAI UNIVERSITY SCHOOL OF MEDICINE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULES; PROTEINS;

BINDING ABILITIES; HIGH QUALITY; MOLECULAR GROUPS; SMALL MOLECULES; SPECIFIC BINDING; SPECIFIC SITES; X-RAY STRUCTURE;

BINDING SITES;

AMINO ACID; DRUG; PORPHYRIN; PROTEIN;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM; PROTEIN TERTIARY STRUCTURE;

AMINO ACIDS; BINDING SITES; MODELS, MOLECULAR; PHARMACEUTICAL PREPARATIONS; PORPHYRINS; PROTEIN STRUCTURE, TERTIARY; PROTEINS;

EID: 52049121294     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci800113c     Document Type: Article

References (14)

1. Berman, H. M.; Westbrook, J.; Fenz, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The protein data bank. Nucleic Acids. Res. 2000, 28, 235-242.
2. Walker, J. E.; Saraste, M.; Runswick, M. J.; Gay, N. J. Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1982, 1, 945-951.
3. Brakoulias, A.; Jackson, R. M. Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: an automated all-against-all structural comparison using geometric matching. Proteins 2004, 56, 250-260.
4. Shulman-Peleg, A.; Nussinov, R.; Wolfson, H. J. Recognition of functional sites in protein structures. J. Mol. Biol. 2004, 339, 607-633.
5. Zhang, Z.; Grigorov, M. G. Similarity networks of protein binding sites. Proteins 2006, 62, 470-478.
6. Davies, J. R.; Jackson, R. M.; Mardia, K. V.; Taylor, C. C. The Poisson Index: a new probabilistic model for protein ligand binding site similarity. Bioinformatics 2007, 23, 3001-3008.
7. Konc, J.; Janezic, D. Protein-protein binding-sites prediction by protein surface structure conservation. J. Chem. Inf. Model. 2007, 47, 940-944.
8. Soga, S.; Shirai, H.; Kobori, M.; Hirayama, N. Use of amino acid composition to predict ligand-binding sites. J. Chem. Inf. Model. 2007, 47, 400-406.
9. Soga, S.; Shirai, H.; Kobori, M.; Hirayama, N. Identification of the druggable concavity in homology models using the PLB index. J. Chem. Inf. Model. 2007, 47, 2287-2292.
10. Altschul, S. F.; Gish, W.; Miller, W.; Myers, E. W.; Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 1990, 215, 403-410.
11. MOE (Molecular Operating Environment), version 2006.0801; Chemical Computing Group Inc.: Montreal, Quebec, Canada, 2006.
12. Jarvis, R. A.; Patrick, E. A. Clustering using a similarity measure based on shared near neighbors. IEEE Trans. Comput. 1973, C22, 1025-1034.
13. Wildman, S. A.; Crippen, G. M. Prediction of Physiochemical Parameters by Atomic Contributions. J. Chem. Inf. Comput. Sci. 1999, 39, 868-873.
14. Gutteridge, A.; Thornton, J. M. Understanding nature's catalytic toolkit. Trends Biochem. Sci. 2005, 30, 622-629.