Surface-based protein binding pocket similarity

Proteins: Structure, Function and Bioinformatics

Volumn 79, Issue 9, 2011, Pages 2746-2763

  Spitzer, Russell ^a   Cleves, Ann E ^a   Jain, Ajay N ^a  

^a San Francisco   (United States)

Author keywords

ATP; Binding site; GKST loop; Kinases; Protein similarity

Indexed keywords

ADENOSINE TRIPHOSPHATE; PROTEIN KINASE;

ARTICLE; BINDING SITE; LIGAND BINDING; MORPHOLOGY; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN STRUCTURE;

ALGORITHMS; AMINO ACID SEQUENCE; BINDING SITES; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; HUMANS; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEIN KINASES; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 80051567982     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.23103     Document Type: Article

References (28)

1. Jain AN. Morphological similarity: a 3D molecular similarity method correlated with protein-ligand recognition. J Comput Aided Mol Des 2000; 14: 199-213.
2. Jain AN. Ligand-based structural hypotheses for virtual screening. J Med Chem 2004; 47: 947-961.
3. Jain AN, Harris NL, Park JY. Quantitative binding site model generation: compass applied to multiple chemotypes targeting the 5-HT1A receptor. J Med Chem 1995; 38: 1295-1308.
4. Langham JJ, Cleves AE, Spitzer R, Kirshner D, Jain AN. Physical binding pocket induction for affinity prediction. J Med Chem 2009; 52: 6107-6125.
5. Nicholls A, McGaughey GB, Sheridan RP, Good AC, Warren G, Mathieu M, Muchmore SW, Brown SP, Grant JA, Haigh JA, Nevins N, Jain AN, Kelley B. Molecular shape and medicinal chemistry: a perspective. J Med Chem 2010; 53: 3862-3886.
6. Kahraman A, Morris RJ, Laskowski RA, Thornton JM. Shape variation in protein binding pockets and their ligands. J Mol Biol 2007; 368: 283-301.
7. Hoffmann B, Zaslavskiy M, Vert JP, Stoven V. A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction. BMC Bioinformatics 2010; 11: 99.
8. Yeturu K, Chandra N. PocketMatch: a new algorithm to compare binding sites in protein structures. BMC Bioinformatics 2008; 9: 543.
9. Fabian MA, Biggs WH, III, Treiber DK, Atteridge CE, Azimioara MD, Benedetti MG, Carter TA, Ciceri P, Edeen PT, Floyd M, Ford JM, Galvin M, Gerlach JL, Grotzfeld RM, Herrgard S, Insko DE, Insko MA, Lai AG, Lelias JM, Mehta SA, Milanov ZV, Velasco AM, Wodicka LM, Patel HK, Zarrinkar PP, Lockhart DJ. A small molecule-kinase interaction map for clinical kinase inhibitors. Nat Biotechnol 2005; 23: 329-336.
10. Kinnings SL, Jackson RM. Binding site similarity analysis for the functional classification of the protein kinase family. J Chem Inf Model 2009; 49: 318-329.
11. Hu L, Benson ML, Smith RD, Lerner MG, Carlson HA. Binding MOAD (Mother Of All Databases). Proteins 2005; 60: 333-340.
12. Rose PW, Beran B, Bi C, Bluhm WF, Dimitropoulos D, Goodsell DS, Prlic A, Quesada M, Quinn GB, Westbrook JD, Young J, Yukich B, Zardecki C, Berman HM, Bourne PE. The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res 2011: 39(Database issue) D392-D401.
13. Caetano-Anolles G, Kim HS, Mittenthal JE. The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture. Proc Natl Acad Sci USA 2007; 104: 9358-9363.
14. Hanks SK, Quinn AM, Hunter T. The protein kinase family: conserved features and deduced phylogeny of the catalytic domains. Science 1988; 241: 42-52.
15. Meng EC, Pettersen EF, Couch GS, Huang CC, Ferrin TE. Tools for integrated sequence-structure analysis with UCSF Chimera. BMC Bioinformatics 2006; 7: 339.
16. Hanks SK, Hunter T. Protein kinases 6. The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification. FASEB J 1995; 9: 576-596.
17. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23: 2947-2948.
18. Xie L, Bourne PE. A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery. Bioinformatics 2009; 25: i305-312.
19. Holm L, Sander C. Dali: a network tool for protein structure comparison. Trends Biochem Sci 1995; 20: 478-480.
20. Holm L, Sander C. Dali/FSSP classification of three-dimensional protein folds. Nucleic Acids Res 1997; 25: 231-234.
21. Shindyalov IN, Bourne PE. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 1998; 11: 739-747.
22. Shindyalov IN, Bourne PE. An alternative view of protein fold space. Proteins 2000; 38: 247-260.
23. Shindyalov IN, Bourne PE. A database and tools for 3-D protein structure comparison and alignment using the combinatorial extension (CE) algorithm. Nucleic Acids Res 2001; 29: 228-229.
24. Wu S, Liang MP, Altman RB. The SeqFEATURE library of 3D functional site models: comparison to existing methods and applications to protein function annotation. Genome Biol 2008; 9: R8.
25. Polacco BJ, Babbitt PC. Automated discovery of 3D motifs for protein function annotation. Bioinformatics 2006; 22: 723-730.
26. Weill N, Rognan D. Alignment-free ultra-high-throughput comparison of druggable protein-ligand binding sites. J Chem Inf Model 2010; 50: 123-135.
27. Jain AN. Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation. J Comput Aided Mol Des 2009; 23: 355-374.
28. Hendrickson WA. Impact of structures from the protein structure initiative. Structure 2007; 15: 1528-1529.