Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets

BMC Bioinformatics

Volumn 13, Issue 1, 2012, Pages

  Ashford, Paul ^a   Moss, David S ^a   Alex, Alexander ^b   Yeap, Siew K ^b   Povia, Alice ^a   Nobeli, Irene ^a   Williams, Mark A ^a  

^a UNIVERSITY OF LONDON   (United Kingdom)

^b PFIZER GLOBAL RESEARCH AND DEVELOPMENT   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL TOOLS; HOMOLOGOUS STRUCTURES; PREDICTION ALGORITHMS; PROBABILISTIC ANALYSIS; PROTEIN-PROTEIN INTERFACE; RATIONAL DRUG DESIGNS; SMALL-MOLECULE DRUGS; STRUCTURAL ALIGNMENTS;

ALGORITHMS; BINDING SITES; COMPUTATIONAL METHODS; CONFORMATIONS; FORECASTING; LIGANDS; MOLECULAR GRAPHICS; VISUALIZATION;

PROTEINS;

INTERLEUKIN 2; LIGAND; PROTEIN; PROTEIN KINASE;

ALGORITHM; ANIMAL; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; DRUG DESIGN; HUMAN; METABOLISM; PROTEIN CONFORMATION; SURFACE PROPERTY;

ALGORITHMS; ANIMALS; DRUG DESIGN; HUMANS; INTERLEUKIN-2; LIGANDS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN KINASES; PROTEINS; SOFTWARE; SURFACE PROPERTIES;

EID: 84863393146     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-39     Document Type: Article

References (39)

1. Brady G, Stouten P. Fast prediction and visualization of protein binding pockets with PASS. J Comput Aided Mol Des 2000, 14:383-401. 10.1023/A:1008124202956, 10815774.
2. Hendlich M, Rippmann F, Barnickel G. LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. J Mol Graph Model 1997, 15:359-363. 10.1016/S1093-3263(98)00002-3, 9704298.
3. Levitt D, Banaszak L. POCKET: A computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. J Mol Graph 1992, 10:229-234. 10.1016/0263-7855(92)80074-N, 1476996.
4. Weisel M, Proschak E, Schneider G. PocketPicker: analysis of ligand binding-sites with shape descriptors. Chem Cent J 2007, 1:7. 10.1186/1752-153X-1-7, 1994066, 17880740.
5. Laskowski RA. SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J Mol Graph 1995, 13:323-330. 10.1016/0263-7855(95)00073-9, 8603061.
6. Liang J, Edelsbrunner H, Woodward C. Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci 1998, 7:1884-1897. 10.1002/pro.5560070905, 2144175, 9761470.
7. Schmidtke P, Guilloux VL, Maupetit J, Tuffery P. fpocket: online tools for protein ensemble pocket detection and tracking. Nucleic Acids Res 2010, 38:W582-W589. 10.1093/nar/gkq383, 2896101, 20478829.
8. 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.
9. 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.
10. Laurie A, Jackson R. Q-Site Finder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 2005, 21:1908-1916. 10.1093/bioinformatics/bti315, 15701681.
11. Huang B. MetaPocket: a meta approach to improve protein ligand binding site prediction. OMICS 2009, 13:325-330. 10.1089/omi.2009.0045, 19645590.
12. Chen K, Mizianty MJ, Gao J, Kurgan L. A critical comparative assessment of predictions of protein-binding sites for biologically relevant organic compounds. Structure 2011, 19:613-621.
13. McCammon JA, Harvey SC. Dynamics of proteins and nucleic acids 1987, Cambridge: Cambridge University Press.
14. Keskin O, Gursoy A, Ma B, Nussinov R. Principles of protein-protein interactions: what are the preferred ways for proteins to interact?. Chem Rev 2008, 108:1225-1244. 10.1021/cr040409x, 18355092.
15. McCammon JA, Gelin BR, Karplus M. Dynamics of folded proteins. Nature 1977, 267:585-590. 10.1038/267585a0, 301613.
16. Karplus M, McCammon J. Molecular dynamics simulations of biomolecules. Nat Struct Biol 2002, 9:646-652. 10.1038/nsb0902-646, 12198485.
17. Amadei A, Linssen A, Berendsen H. Essential dynamics of proteins. PROTEINS: Struct Funct Gen 1993, 17:412-425. 10.1002/prot.340170408, 8108382.
18. Brooks B, Karplus M. Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme. P Natl Acad Sci USA 1985, 82:4995-4999. 10.1073/pnas.82.15.4995, 3860838.
19. de Groot B, van Aalten D, Scheek R, Amadei A, Vriend G, Berendsen H. Prediction of protein conformational freedom from distance constraints. Proteins 1997, 29:240-251. 10.1002/(SICI)1097-0134(199710)29:2<240::AID-PROT11>3.0.CO;2-O, 9329088.
20. Seeliger D, Haas J, de Groot BL. Geometry-based sampling of conformational transitions in proteins. Structure 2007, 15:1482-1492. 10.1016/j.str.2007.09.017, 17997973.
21. Leo-Macias A, Lopez-Romero P, Lupyan D, Zerbino D, Ortiz AR. An analysis of core deformations in protein superfamilies. Biophys J 2005, 88:1291-1299. 10.1529/biophysj.104.052449, 1305131, 15542556.
22. Via A, Ferre F, Brannetti B, Helmer-Citterich M. Protein surface similarities: a survey of methods to describe and compare protein surfaces. Cell Mol Life Sci 2000, 57:1970-1977. 10.1007/PL00000677, 11215522.
23. Kahraman A, Morris RJ, Laskowski RA, Thornton JM. Shape variation in protein binding pockets and their ligands. J Mol Biol 2007, 368:283-301. 10.1016/j.jmb.2007.01.086, 17337005.
24. Campbell S, Gold N, Jackson R, Westhead D. Ligand binding: functional site location, similarity and docking. Curr Opin Struct Biol 2003, 13:389-395. 10.1016/S0959-440X(03)00075-7, 12831892.
25. Eyrisch S, Helms V. Transient Pockets on Protein Surfaces Involved in Protein Interaction. J Med Chem 2007, 50:3457-3464. 10.1021/jm070095g, 17602601.
26. Eyrisch S, Helms V. What induces pocket openings on protein surface patches involved in protein-protein interactions?. J Comput Aided Mol Des 2009, 23:73-86. 10.1007/s10822-008-9239-y, 18777159.
27. Schmidtke P, Bidon-Chanal A, Luque FJ, Barril X. MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories. Bioinformatics 2011, 27:3276-3285. 10.1093/bioinformatics/btr550, 21967761.
28. Halgren TA. Identifying and characterizing binding sites and assessing druggability. J Chem Inf Model 2009, 49:377-389. 10.1021/ci800324m, 19434839.
29. Goldman JM, Melo JV. Chronic myeloid leukemia-advances in biology and new approaches to treatment. N Engl J Med 2003, 349:1451-1464. 10.1056/NEJMra020777, 14534339.
30. Wells J, McClendon C. Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 2007, 450:1001-1009. 10.1038/nature06526, 18075579.
31. Bourgeas R, Basse MJ, Morelli X, Roche P. Atomic analysis of protein-protein interfaces with known inhibitors: the 2P2I database. PLoS One 2010, 5:e9598. 10.1371/journal.pone.0009598, 2834754, 20231898.
32. Arkin M, Randal M, DeLano W, Hyde J, Luong T, Oslob J, Raphael D, Taylor L, Wang J, McDowell R. Binding of small molecules to an adaptive protein-protein interface. P Natl Acad Sci USA 2003, 100:1603-1608. 10.1073/pnas.252756299, 12582206.
33. Davis FP, Sali A. The overlap of small molecule and protein binding sites within families of protein structures. PLoS Comput Biol 2010, 6:e1000668. 10.1371/journal.pcbi.1000668, 2816688, 20140189.
34. Berman H, Westbrook J, Feng Z, Gilliland G, Bhat T, Weissig H, Shindyalov I, Bourne P. The Protein Data Bank. Nucleic Acids Res 2000, 28:235-242. 10.1093/nar/28.1.235, 102472, 10592235.
35. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. UCSF Chimera-a visualization system for exploratory research and analysis. J Comput Chem 2004, 25:1605-1612. 10.1002/jcc.20084, 15264254.
36. Orengo C, Michie A, Jones S, Jones D, Swindells M, Thornton J. CATH-a hierarchic classification of protein domain structures. Structure 1997, 5:1093-1108. 10.1016/S0969-2126(97)00260-8, 9309224.
37. Thompson JD, Gibson TJ, Higgins DG. Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics 2002, Chapter 2: Unit 2.3.
38. Konagurthu AS, Whisstock JC, Stuckey PJ, Lesk AM. MUSTANG: a multiple structural alignment algorithm. Proteins 2006, 64:559-574. 10.1002/prot.20921, 16736488.
39. Holland RCG, Down TA, Pocock M, Prlić A, Huen D, James K, Foisy S, Dräger A, Yates A, Heuer M, Schreiber MJ. BioJava: an open-source framework for bioinformatics. Bioinformatics 2008, 24:2096-2097. 10.1093/bioinformatics/btn397, 2530884, 18689808.