Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities

BMC Bioinformatics

Volumn 13, Issue SUPPL.4, 2012, Pages

  Bianchi, Valerio ^a   Gherardini, Pier Federico ^a   Helmer Citterich, Manuela ^a   Ausiello, Gabriele ^a  

^a UNIVERSITY OF ROME TOR VERGATA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING POCKETS; CHEMICAL FRAGMENTS; HIGH QUALITY; KNOWLEDGE-BASED METHODS; LIGAND-BINDING RESIDUES; LIGAND-BINDING SITES; NON-REDUNDANT; PROTEIN STRUCTURES; PROTEIN SURFACE; PROTEIN-LIGAND COMPLEXES; QUERY PROTEINS; REAL-WORLD APPLICATION; STRUCTURAL MOTIFS; STRUCTURAL SIMILARITY;

BINDING SITES; COMPLEXATION; KNOWLEDGE BASED SYSTEMS; LIGANDS;

PROTEINS;

LIGAND; PROTEIN;

ALGORITHM; ANIMAL; ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; KNOWLEDGE BASE; METABOLISM; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DATABASE; PROTEIN TERTIARY STRUCTURE;

ALGORITHMS; ANIMALS; BINDING SITES; DATABASES, PROTEIN; KNOWLEDGE BASES; LIGANDS; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; PROTEINS;

EID: 84864936114     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-S4-S17     Document Type: Article

References (33)

1. Gherardini PF, Helmer-Citterich M. Structure-based function prediction: approaches and applications. Brief Funct Genomic Proteomic 2008, 7:291-302. 10.1093/bfgp/eln030, 18599513.
2. Laskowski RA. SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J Mol Graph 1995, 13:323-330. 307-308, 10.1016/0263-7855(95)00073-9, 8603061.
3. Huang B, Schroeder M. LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Struct Biol 2006, 6:19. 10.1186/1472-6807-6-19, 1601958, 16995956.
4. Capra JA, Laskowski RA, Thornton JM, Singh M, Funkhouser TA. Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. PLoS Comput Biol 2009, 5:e1000585. 10.1371/journal.pcbi.1000585, 2777313, 19997483.
5. Peters KP, Fauck J, Frömmel C. The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria. J Mol Biol 1996, 256:201-213. 10.1006/jmbi.1996.0077, 8609611.
6. Tan KP, Varadarajan R, Madhusudhan MS. DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins. Nucleic Acids Res 2011, 39(Suppl 2):W242-248. 3125764, 21576233.
7. Laskowski RA, Luscombe NM, Swindells MB, Thornton JM. Protein clefts in molecular recognition and function. Protein Sci 1996, 5:2438-2452. 2143314, 8976552.
8. Dessailly BH, Lensink MF, Orengo CA, Wodak SJ. LigASite--a database of biologically relevant binding sites in proteins with known apo-structures. Nucleic Acids Res 2008, 36:D667-D673. 2238865, 17933762.
9. Morita M, Nakamura S, Shimizu K. Highly accurate method for ligand-binding site prediction in unbound state (apo) protein structures. Proteins 2008, 73:468-479. 10.1002/prot.22067, 18452211.
10. Laurie ATR, Jackson RM. Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 2005, 21:1908-1916. 10.1093/bioinformatics/bti315, 15701681.
11. Hernandez M, Ghersi D, Sanchez R. SITEHOUND-web: a server for ligand binding site identification in protein structures. Nucleic Acids Res 2009, 37:W413-W416. 10.1093/nar/gkp281, 2703923, 19398430.
12. Amitai G, Shemesh A, Sitbon E, et al. Network analysis of protein structures identifies functional residues. J Mol Biol 2004, 344:1135-1146. 10.1016/j.jmb.2004.10.055, 15544817.
13. Ondrechen MJ, Clifton JG, Ringe D. THEMATICS: a simple computational predictor of enzyme function from structure. Proc Natl Acad Sci USA 2001, 98:12473-12478. 10.1073/pnas.211436698, 60078, 11606719.
14. Ota M, Kinoshita K, Nishikawa K. Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation. J Mol Biol 2003, 327:1053-1064. 10.1016/S0022-2836(03)00207-9, 12662930.
15. Mehio W, Kemp GJL, Taylor P, Walkinshaw MD. Identification of protein binding surfaces using surface triplet propensities. Bioinformatics 2010, 26:2549-2555. 10.1093/bioinformatics/btq490, 20819959.
16. Wass MN, Kelley LA, Sternberg MJE. 3DLigandSite: predicting ligand-binding sites using similar structures. Nucleic Acids Res 2010, (38 Web Server):W469-W473. 2896164, 20513649.
17. Brylinski M, Skolnick J. A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proc Natl Acad Sci USA 2008, 105:129-134. 10.1073/pnas.0707684105, 2224172, 18165317.
18. Lopez G, Valencia A, Tress ML. firestar--prediction of functionally important residues using structural templates and alignment reliability. Nucleic Acids Res 2007, (35 Web Server):W573-W577. 1933227, 17584799.
19. Kasahara K, Kinoshita K, Takagi T. Ligand-binding site prediction of proteins based on known fragment-fragment interactions. Bioinformatics 2010, 26:1493-1499. 10.1093/bioinformatics/btq232, 2881410, 20472546.
20. Ramensky V, Sobol A, Zaitseva N, Rubinov A, Zosimov V. A novel approach to local similarity of protein binding sites substantially improves computational drug design results. Proteins 2007, 69:349-357. 10.1002/prot.21487, 17623865.
21. Verdonk ML, Cole JC, Taylor R. SuperStar: a knowledge-based approach for identifying interaction sites in proteins. J Mol Biol 1999, 289:1093-1108. 10.1006/jmbi.1999.2809, 10369784.
22. Ausiello G, Gherardini PF, Gatti E, Incani O, Helmer-Citterich M. Structural motifs recurring in different folds recognize the same ligand fragments. BMC Bioinformatics 2009, 10:182. 10.1186/1471-2105-10-182, 2704211, 19527512.
23. Gherardini PF, Ausiello G, Russell RB, Helmer-Citterich M. Modular architecture of nucleotide-binding pockets. Nucleic Acids Res 2010, 38:3809-3816. 10.1093/nar/gkq090, 2887960, 20185567.
24. Ausiello G, Via A, Helmer-Citterich M. Query3d: a new method for high-throughput analysis of functional residues in protein structures. BMC Bioinformatics 2005, 6(Suppl 4):S5. 10.1186/1471-2105-6-S4-S5, 1866380, 16351754.
25. Gherardini PF, Ausiello G, Helmer-Citterich M. Superpose3D: a local structural comparison program that allows for user-defined structure representations. PloS One 2010, 5:e11988. 10.1371/journal.pone.0011988, 2916828, 20700534.
26. Villar HO, Kauvar LM. Amino acid preferences at protein binding sites. FEBS Lett 1994, 349:125-130. 10.1016/0014-5793(94)00648-2, 8045288.
27. Q-SiteFinder Webserver. , http://www.modelling.leeds.ac.uk/qsitefinder/
28. Blastclust Sequence Clusters. , ftp://resources.rcsb.org/sequence/clusters/
29. Gold ND, Jackson RM. Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships. J Mol Biol 2006, 355:1112-1124. 10.1016/j.jmb.2005.11.044, 16359705.
30. Gregory DS, Martin AC, Cheetham JC, Rees AR. The prediction and characterization of metal binding sites in proteins. Protein Eng 1993, 6:29-35. 10.1093/protein/6.1.29, 8433968.
31. Ausiello G, Zanzoni A, Peluso D, Via A, Helmer-Citterich M. pdbFun: mass selection and fast comparison of annotated PDB residues. Nucleic Acids Res 2005, (33 Web Server):W133-W137. 1160259, 15980442.
32. Henrick K, Thornton JM. PQS: a protein quaternary structure file server. Trends Biochem Sci 1998, 23:358. 10.1016/S0968-0004(98)01253-5, 9787643.
33. Wang G, Dunbrack RL. PISCES: a protein sequence culling server. Bioinformatics 2003, 19:1589-1591. 10.1093/bioinformatics/btg224, 12912846.