ProBiS-2012: Web server and web services for detection of structurally similar binding sites in proteins

Nucleic Acids Research

Volumn 40, Issue W1, 2012, Pages

  Konc, Janez ^a   Janežič, Dušanka ^a  

^a NATIONAL INSTITUTE OF CHEMISTRY   (Slovenia)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BINDING SITE; CALCULATION; COMPARATIVE STUDY; COMPUTER INTERFACE; COMPUTER PROGRAM; DATA BASE; INTERNET; PRIORITY JOURNAL; PROBIS-DATABASE; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN STRUCTURE; WEB SERVER;

ALGORITHMS; BINDING SITES; ENZYME INHIBITORS; INTERNET; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; SOFTWARE;

EID: 84864485292     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks435     Document Type: Article

References (37)

1. Jaroszewski, L., Li, Z., Krishna, S.S., Bakolitsa, C., Wooley, J., Deacon, A.M., Wilson, I.A. and Godzik, A. (2009) Exploration of uncharted regions of the protein universe. PLoS Biol., 7, e1000205.
2. Musiani, F., Bellucci, M. and Ciurli, S. (2011) Model structures of Helicobacter pylori UreD(H) domains: a putative molecular recognition platform. J. Chem. Inf. Model., 51, 1513-1520.
3. Wong, M.T., Choi, S.B., Kuan, C.S., Chua, S.L., Chang, C.H., Normi, Y.M., Too, W.C., Wahab, H.A. and Few, L.L. (2012) Structural modeling and biochemical characterization of recombinant KPN-02809, a zinc-dependent metalloprotease from Klebsiella pneumoniae MGH 78578. Int. J. Mol. Sci., 13, 901-917.
4. Kar, G., Keskin, O., Nussinov, R. and Gursoy, A. (2012) Human proteome-scale structural modeling of E2-E3 interactions exploiting interface motifs. J. Proteome Res., 11, 1196-1207.
5. Ashburn, T.T. and Thor, K.B. (2004) Drug repositioning: identifying and developing new uses for existing drugs. Nat. Rev. Drug. Discov., 3, 673-683.
6. Haupt, V.J. and Schroeder, M. (2011) Old friends in new guise: repositioning of known drugs with structural bioinformatics. Brief. Bioinform., 12, 312-326.
7. Kinnings, S.L., Liu, N., Buchmeier, N., Tonge, P.J., Xie, L. and Bourne, P.E. (2009) Drug discovery using chemical systems biology: repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis. PLoS Comput. Biol., 5, e1000423.
8. Xie, L., Evangelidis, T. and Bourne, P.E. (2011) Drug discovery using chemical systems biology: weak inhibition of multiple kinases may contribute to the anti-cancer effect of nelfinavir. PLoS Comput. Biol., 7, e1002037.
9. Defranchi, E., Schalon, C., Messa, M., Onofri, F., Benfenati, F. and Rognan, D. (2010) Binding of protein kinase inhibitors to synapsin I inferred from pair-wise binding site similarity measurements. PLoS One, 5, e12214.
10. Russell, R.B. (1998) Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution. J. Mol. Biol., 279, 1211-1227.
11. 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.
12. Ito, J., Tabei, Y., Shimizu, K., Tsuda, K. and Tomii, K. (2012) PoSSuM: a database of similar protein-ligand binding and putative pockets. Nucleic Acids Res., 40, D541-D548.
13. Shulman-Peleg, A., Shatsky, M., Nussinov, R. and Wolfson, H.J. (2008) MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions. Nucleic Acids Res., 36, W260-W264.
14. Ausiello, G., Gherardini, P.F., Marcatili, P., Tramontano, A., Via, A. and Helmer-Citterich, M. (2008) FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures. BMC Bioinformatics, 9, S2.
15. Parca, L., Mangone, I., Gherardini, P.F., Ausiello, G. and Helmer-Citterich, M. (2011) Phosfinder: a web server for the identification of phosphate-binding sites on protein structures. Nucleic Acids Res., 39, W278-W282.
16. Regad, L., Saladin, A., Maupetit, J., Geneix, C. and Camproux, A.C. (2011) SA-Mot: a web server for the identification of motifs of interest extracted from protein loops. Nucleic Acids Res., 39, W203-W209.
17. Shirvanyants, D., Alexandrova, A.N. and Dokholyan, N.V. (2011) Rigid substructure search. Bioinformatics, 27, 1327-1329.
18. Jambon, M., Andrieu, O., Combet, C., Deleage, G., Delfaud, F. and Geourjon, C. (2005) The SuMo server: 3D search for protein functional sites. Bioinformatics, 21, 3929-3930.
19. Stark, A. and Russell, R.B. (2003) Annotation in three dimensions. PINTS: patterns in non-homologous tertiary structures. Nucleic Acids Res., 31, 3341-3344.
20. Goyal, K., Mohanty, D. and Mande, S.C. (2007) PAR-3D: a server to predict protein active site residues. Nucleic Acids Res., 35, W503-W505.
21. Angaran, S., Bock, M.E., Garutti, C. and Guerra, C. (2009) MolLoc: a web tool for the local structural alignment of molecular surfaces. Nucleic Acids Res., 37, W565-W570.
22. Ren, J., Xie, L., Li, W.W. and Bourne, P.E. (2010) SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison. Nucleic Acids Res., 38, W441-W444.
23. von Eichborn, J., Murgueitio, M.S., Dunkel, M., Koerner, S., Bourne, P.E. and Preissner, R. (2011) PROMISCUOUS: a database for network-based drug-repositioning. Nucleic Acids Res., 39, D1060-D1066.
24. Luo, H., Chen, J., Shi, L., Mikailov, M., Zhu, H., Wang, K., He, L. and Yang, L. (2011) DRAR-CPI: a server for identifying drug repositioning potential and adverse drug reactions via the chemical-protein interactome. Nucleic Acids Res., 39, W492-W498.
25. Konc, J. and Janezic, D. (2010) ProBiS: a web server for detection of structurally similar protein binding sites. Nucleic Acids Res., 38, W436-W440.
26. Konc, J. and Janezic, D. (2010) ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment. Bioinformatics, 26, 1160-1168.
27. Konc, J., Cesnik, T., Trykowska Konc, J., Penca, M. and Janezic, D. (2012) ProBiS-Database: precalculated binding site similarities and local pairwise alignments of PDB structures. J. Chem. Inf. Model., 52, 604-612.
28. 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.
29. Konc, J. and Janezic, D. (2007) An improved branch and bound algorithm for the maximum clique problem. MATCH Commun. Math. Comput. Chem., 58, 569-590.
30. Fielding, R.T. and Taylor, R.N. (2002) Principled design of the modern web architecture. ACM Trans Internet. Technol., 2, 115-150.
31. Velankar, S., McNeil, P., Mittard-Runte, V., Suarez, A., Barrell, D., Apweiler, R. and Henrick, K. (2005) E-MSD: an integrated data resource for bioinformatics. Nucleic Acids Res., 33, D262-D265.
32. Skedelj, V., Tomasic, T., Masic, L.P. and Zega, A. (2011) ATP-binding site of bacterial enzymes as a target for antibacterial drug design. J. Med. Chem., 54, 915-929.
33. Triola, G., Wetzel, S., Ellinger, B., Koch, M.A., Hubel, K., Rauh, D. and Waldmann, H. (2009) ATP competitive inhibitors of D-alanine-D-alanine ligase based on protein kinase inhibitor scaffolds. Bioorg. Med. Chem., 17, 1079-1087.
34. Huang, D., Zhou, T., Lafleur, K., Nevado, C. and Caflisch, A. (2010) Kinase selectivity potential for inhibitors targeting the ATP binding site: a network analysis. Bioinformatics, 26, 198-204.
35. Fedorov, O., Huber, K., Eisenreich, A., Filippakopoulos, P., King, O., Bullock, A.N., Szklarczyk, D., Jensen, L.J., Fabbro, D., Trappe, J. et al. (2011) Specific CLK inhibitors from a novel chemotype for regulation of alternative splicing. Chem. Biol., 18, 67-76.
36. Ye, Y. and Godzik, A. (2003) Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics, 19(Suppl. 2), 246-255.
37. Holm, L. and Park, J. (2000) DaliLite workbench for protein structure comparison. Bioinformatics, 16, 566-567.