PoSSuM: A database of similar protein-ligand binding and putative pockets

Nucleic Acids Research

Volumn 40, Issue D1, 2012, Pages

  Ito, Jun Ichi ^a,b   Tabei, Yasuo ^c   Shimizu, Kana ^b   Tsuda, Koji ^b,c   Tomii, Kentaro ^a,b  

^a UNIVERSITY OF TOKYO   (Japan)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; BINDING SITE; COMPUTER INTERFACE; COMPUTER PROGRAM; CONTROLLED STUDY; DRUG DESIGN; LIGAND BINDING; POCKET SIMILARITY SEARCH USING MULTIPLE SKETCHES; PREDICTION AND FORECASTING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATA BANK; PROTEIN DATABASE; PROTEIN FUNCTION; PROTEIN LIGAND BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEIN TARGETING;

BINDING SITES; DATABASES, PROTEIN; DRUG DESIGN; LIGANDS; MOLECULAR SEQUENCE ANNOTATION; PROTEIN CONFORMATION; USER-COMPUTER INTERFACE;

EID: 84862181488     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1130     Document Type: Article

References (29)

1. Schmitt,S., Kuhn,D. and Klebe,G. (2002) A new method to detect related function among proteins independent of sequence and fold homology. J. Mol. Biol., 323, 387-406. (Pubitemid 35283699)
2. Shulman-Peleg,A., Nussinov,R. and Wolfson,H.J. (2004) Recognition of functional sites in protein structures. J. Mol. Biol., 339, 607-633. (Pubitemid 38625909)
3. Gold,N.D. and Jackson,R.M. (2006) Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships. J. Mol. Biol., 355, 1112-1124. (Pubitemid 43012151)
4. Kinoshita,K., Murakami,Y. and Nakamura,H. (2007) eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape. Nucleic Acids Res., 35, W398-W402.
5. Kinjo,A.R. and Nakamura,H. (2007) Similarity search for local protein structures at atomic resolution by exploiting a database management system. Biophysics, 3, 75-84.
6. Minai,R., Matsuo,Y., Onuki,H. and Hirota,H. (2008) Method for comparing the structures of protein ligand-binding sites and application for predicting protein-drug interactions. Proteins, 72, 367-381. (Pubitemid 351809174)
7. 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. (Pubitemid 30047768)
8. Laskowski,R.A. (1995) SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J. Mol. Graph, 13, 323-330, 307-328.
9. Hendlich,M., Rippmann,F. and Barnickel,G. (1997) LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. J. Mol. Graph Model, 15, 359-363, 389.
10. Dundas,J., Ouyang,Z., Tseng,J., Binkowski,A., Turpaz,Y. and Liang,J. (2006) CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res., 34, W116-W118. (Pubitemid 44529746)
11. An,J., Totrov,M. and Abagyan,R. (2005) Pocketome via comprehensive identification and classification of ligand binding envelopes. Mol. Cell. Proteomics, 4, 752-761. (Pubitemid 40873004)
12. Capra,J.A., Laskowski,R.A., Thornton,J.M., Singh,M. and Funkhouser,T.A. (2009) Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. PLoS Comput. Biol., 5, e1000585.
13. Kawabata,T. (2010) Detection of multiscale pockets on protein surfaces using mathematical morphology. Proteins, 78, 1195-1211.
14. Yin,S., Proctor,E.A., Lugovskoy,A.A. and Dokholyan,N.V. (2009) Fast screening of protein surfaces using geometric invariant fingerprints. Proc. Natl Acad. Sci. USA, 106, 16622-16626.
15. Weill,N. and Rognan,D. (2010) Alignment-free ultra-high-throughput comparison of druggable protein-ligand binding sites. J. Chem. Inf. Model, 50, 123-135.
16. Sciabola,S., Stanton,R.V., Mills,J.E., Flocco,M.M., Baroni,M., Cruciani,G., Perruccio,F. and Mason,J.S. (2010) High-throughput virtual screening of proteins using GRID molecular interaction fields. J. Chem. Inf. Model, 50, 155-169.
17. Xiong,B., Wu,J., Burk,D.L., Xue,M., Jiang,H. and Shen,J. (2010) BSSF: a fingerprint based ultrafast binding site similarity search and function analysis server. BMC Bioinformatics, 11, 47.
18. Tabei,Y., Uno,T., Sugiyama,M. and Tsuda,K. (2010) Single versus multiple sorting for all pairs similarity search, In the 2nd Asian Conference on Machine Learning (ACML2010), Tokyo, Japan, 13, pp. 145-160.
19. Greene,L.H., Lewis,T.E., Addou,S., Cuff,A., Dallman,T., Dibley,M., Redfern,O., Pearl,F., Nambudiry,R., Reid,A. et al. (2007) The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. Nucleic Acids Res., 35, D291-D297. (Pubitemid 46056217)
20. Andreeva,A., Howorth,D., Chandonia,J.M., Brenner,S.E., Hubbard,T.J., Chothia,C. and Murzin,A.G. (2008) Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res., 36, D419-D425. (Pubitemid 351149760)
21. Martin,A.C. (2004) PDBSprotEC: a Web-accessible database linking PDB chains to EC numbers via SwissProt. Bioinformatics, 20, 986-988.
22. The GO Consortium. (2007) The Gene Ontology project in 2008. Nucleic Acids Res., 36, D440-D444.
23. Gold,N.D. and Jackson,R.M. (2006) SitesBase: a database for structure-based protein-ligand binding site comparisons. Nucleic Acids Res., 34, D231-D234.
24. Ito,J., Tabei,Y., Shimizu,K., Tomii,K. and Tsuda,K. PDB-Scale analysis of known and putative ligand binding sites with structural sketches. Proteins, (in press).
25. Uno,T. (2010) Multi-sorting algorithm for finding pairs of similar short substrings from large-scale string data. Knowl. Inf. Syst., 25, 229-251.
26. Zhang,Y. and Skolnick,J. (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res., 33, 2302-2309. (Pubitemid 41439897)
27. Marr,R.A., Guan,H., Rockenstein,E., Kindy,M., Gage,F.H., Verma,I., Masliah,E. and Hersh,L.B. (2004) Neprilysin regulates amyloid Beta peptide levels. J. Mol. Neurosci., 22, 5-11. (Pubitemid 41359010)
28. Baral,P.K., Jajcanin-Jozic,N., Deller,S., Macheroux,P., Abramic,M. and Gruber,K. (2008) The first structure of dipeptidyl-peptidase III provides insight into the catalytic mechanism and mode of substrate binding. J. Biol. Chem., 283, 22316-22324.
29. Davis,F.P. and Sali,A. (2010) The overlap of small molecule and protein binding sites within families of protein structures. PLoS Comput. Biol., 6, e1000668.