APoc: Large-scale identification of similar protein pockets

Bioinformatics

Volumn 29, Issue 5, 2013, Pages 597-604

  Gao, Mu ^a   Skolnick, Jeffrey ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; GUANOSINE TRIPHOSPHATASE; LIGAND; PROTEIN;

ALGORITHM; ARTICLE; BACTERIUM; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; ENZYMOLOGY; METABOLISM; PROTEIN CONFORMATION; STATISTICAL MODEL;

ALGORITHMS; BACTERIA; BACTERIAL PROTEINS; BINDING SITES; GTP PHOSPHOHYDROLASES; LIGANDS; MODELS, MOLECULAR; MODELS, STATISTICAL; PROTEIN CONFORMATION; PROTEINS; SOFTWARE;

EID: 84874754249     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt024     Document Type: Article

References (38)

1. Alberts, B. (2008) Molecular Biology of the Cell. Garland Science, New York.
2. Berman, H. M. et al. (2000) The protein data bank. Nucleic Acids Res., 28, 235-242. (Pubitemid 30047768)
3. Binkowski, T. A. et al. (2003) CASTp: computed atlas of surface topography of proteins. Nucleic Acids Res., 31, 3352-3355. (Pubitemid 37442157)
4. Brylinski, M. and Skolnick, J. (2009) FINDSITELHM: a threading-based approach to ligand homology modeling. PLoS Comp. Biol., 5.
5. Chikhi, R. et al. (2010) Real-time ligand binding pocket database search using local surface descriptors. Proteins, 78, 2007-2028.
6. Davies, J. R. et al. (2007) The Poisson Index: a new probabilistic model for proteinligand binding site similarity. Bioinformatics, 23, 3001-3008. (Pubitemid 350162864)
7. Derigs, U. (1985) The shortest augumenting path method for solving assignment problems - Motivation and computational experience. In: Monma, C. L. (ed.) Algorithms and Software for Optimization. Baltzer, Basel, pp. 57-102.
8. Gao, M. and Skolnick, J. (2010a) iAlign: a method for the structural comparison of protein-protein interfaces. Bioinformatics, 26, 2259-2265.
9. Gao, M. and Skolnick, J. (2010b) Structural space of protein-protein interfaces is degenerate, close to complete, and highly connected. Proc. Natl. Acad. Sci. USA, 107, 22517-22522.
10. Gao, M. and Skolnick, J. (2011) New benchmark metrics for protein-protein docking methods. Proteins, 79, 1623-1634.
11. 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)
12. Gras, S. et al. (2007) Structural insights into a new homodimeric self-activated GTPase family. EMBO Rep., 8, 569-575. (Pubitemid 47214711)
13. Hattori, M. et al. (2010) SIMCOMP/SUBCOMP: chemical structure search servers for network analyses. Nucleic Acids Res., 38, W652-W656.
14. Huang, B. D. and Schroeder, M. (2006) LIGSITE(csc): predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Struct. Biol., 6, 19.
15. Hubbard, T. J. et al. (1998) SCOP, structural classification of proteins database: applications to evaluation of the effectiveness of sequence alignment methods and statistics of protein structural data. Acta Crystallogr. D Bio. Crystallogr., 54, 1147-1154. (Pubitemid 29000170)
16. Humphrey, W. et al. (1996) VMD: visual molecular dynamics. J. Mol. Graphics, 14, 33-38. (Pubitemid 26152973)
17. Kabsch, W. (1976) Solution for best rotation to relate two sets of vectors. Acta Crystallogr. Sect. A, 32, 922-923.
18. Kahraman, A. et al. (2010) On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins. Proteins, 78, 1120-1136.
19. Kahraman, A. et al. (2007) Shape variation in protein binding pockets and their ligands. J. Mol. Biol., 368, 283-301. (Pubitemid 46454307)
20. Laskowski, R. A. (1995) SURFNET - a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J. Mol. Graphics, 13, 323-330.
21. Laskowski, R. A. et al. (1996) Protein clefts in molecular recognition and function. Protein Sci., 5, 2438-2452. (Pubitemid 26424856)
22. Levitt, D. H. and Banaszak, L. J. (1992) POCKET - a computer-graphics method for identifying and displaying protein cavities and their surrounding amino-acids. J. Mol. Graphics, 10, 229-234. (Pubitemid 23018967)
23. Liang, J. et al. (1998) Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci., 7, 1884-1897. (Pubitemid 28432430)
24. Minai, R. et al. (2008) Method for comparing the structures of protein ligand-binding sites and application for predicting protein-drug interactions. Proteins, 72, 367-381. (Pubitemid 351809174)
25. Morris, R. J. et al. (2005) Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons. Bioinformatics, 21, 2347-2355. (Pubitemid 40731589)
26. Najmanovich, R. et al. (2008) Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites. Bioinformatics, 24, I105-I111.
27. Pai, C. H. et al. (2006) Dual binding sites for translocation catalysis by Escherichia coli glutathionylspermidine synthetase. EMBO J., 25, 5970-5982.
28. Perot, S. et al. (2010) Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery. Drug Discov. Today, 15, 656-667.
29. Schmitt, S. et al. (2002) A new method to detect related function among proteins independent of sequence and fold homology. J. Mol. Biol., 323, 387-406. (Pubitemid 35283699)
30. Shulman-Peleg, A. et al. (2004) Recognition of functional sites in protein structures. J. Mol. Biol., 339, 607-633. (Pubitemid 38625909)
31. Skolnick, J. et al. (2009) The continuity of protein structure space is an intrinsic property of proteins. Proc. Natl Acad. Sci. USA, 106, 15690-15695.
32. Sobolev, V. et al. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332. (Pubitemid 29213759)
33. Sudhamsu, J. et al. (2008) The structure of YqeH an AtNOS1/AtNOA1 ortholog that couples GTP hydrolysis to molecular recognition. J. Biol. Chem., 283, 32968-32976.
34. Xie, L. and Bourne, P. E. (2008) Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proc. Natl. Acad. Sci. USA, 105, 5441-5446. (Pubitemid 351753882)
35. Zhang, Y. et al. (2006) On the origin and highly likely completeness of single-domain protein structures. Proc. Natl Acad. Sci. USA, 103, 2605-2610.
36. Zhang, Y. and Skolnick, J. (2004) Scoring function for automated assessment of protein structure template quality. Proteins, 57, 702-710. (Pubitemid 39626992)
37. 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)
38. Zhang, Z. D. and Grigorov, M. H. (2006) Similarity networks of protein binding sites. Proteins, 62, 470-478. (Pubitemid 43054366)