Beta Atomic Contacts: Identifying Critical Specific Contacts in Protein Binding Interfaces

PLoS ONE

Volumn 8, Issue 4, 2013, Pages

  Liu, Qian ^a   Kwoh, Chee Keong ^a   Hoi, Steven C H ^a  

^a NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ATOMIC DENSITY; BETA ATOMIC CONTACT; BETA ATOMIC CONTACT VECTOR; BETA SKELETON; CONTROLLED STUDY; CRYSTALLIZATION; DECISION TREE; DIMERIZATION; ELECTRON; MOLECULAR BIOLOGY; MOLECULAR DYNAMICS; MOLECULAR WEIGHT; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DATABASE; STRUCTURE ANALYSIS;

CRYSTALLOGRAPHY, X-RAY; DECISION TREES; HYDROGEN BONDING; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN STRUCTURE, QUATERNARY; PROTEINS; SUPPORT VECTOR MACHINES;

EID: 84876435567     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0059737     Document Type: Article

References (46)

1. Ofran Y, Rost B, (2003) Analysing six types of protein-protein interfaces. J Mol Biol 325: 377-387.
2. Tsai CJ, Lin SL, Wolfson HJ, Nussinov R, (1996) A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique. J Mol Biol 260: 604-620.
3. Lawrence MC, Colman PM, (1993) Shape complementarity at protein/protein interfaces. J Mol Biol 234: 946-950.
4. Larsen TA, Olson AJ, Goodsell DS, (1998) Morphology of protein-protein interfaces. Structure 6: 421-427.
5. Preissner R, Goede A, Frommel C, (1998) Dictionary of interfaces in proteins (DIP). data bank of complementary molecular surface patches. J Mol Biol 280: 535-550.
6. Korkin D, Davis FP, Sali A, (2005) Localization of protein-binding sites within families of proteins. Protein Sci 14: 2350-2360.
7. Davis FP, Sali A, (2005) PIBASE: a comprehensive database of structurally defined protein interfaces. Bioinformatics 21: 1901-1907.
8. Headd JJ, Ban YEA, Brown P, Edelsbrunner H, Vaidya M, et al. (2007) Protein-protein interfaces: Properties, preferences, and projections. J Proteome Res 6: 2576-2586.
9. Cazals F, Proust F, Bahadur RP, Janin J, (2006) Revisiting the Voronoi description of proteinprotein interfaces. Protein Sci 15: 2082-2092.
10. Bouvier B, Grünberg R, Nilges M, Cazals F, (2009) Shelling the Voronoi interface of protein-protein complexes reveals patterns of residue conservation, dynamics, and composition. Proteins 76: 677-692.
11. Bernauer J, Bahadur RPP, Rodier F, Janin J, Poupon A, (2008) DiMoVo: a voronoi tessellationbased method for discriminating crystallographic and biological protein-protein interactions. Bioinformatics 24: 652-8.
12. Li Z, Li J, (2010) Geometrically centered region: A "wet" model of protein binding hot spots not excluding water molecules. Proteins 78: 3304-3316.
13. McConkey B, Sobolev V, Edelman M, (2002) Quantification of protein surfaces, volumes and atomatom contacts using a constrained Voronoi procedure. Bioinformatics 18: 1365-1373.
14. Cho KI, Kim D, Lee D, (2009) A feature-based approach to modeling protein-protein interaction hot spots. Nucl Acids Res 37: 2672-2687.
15. Zhu H, Domingues FS, Sommer I, Lengauer T (2006) NOXclass: prediction of protein-protein interaction types. BMC Bioinformatics 7.
16. Bahadur RP, Chakrabarti P, Rodier F, Janin J, (2004) A dissection of specific and non-specific protein-protein interfaces. J Mol Biol 336: 943-955.
17. Glaser F, Steinberg DM, Vakser IA, Ben-Tal N, (2001) Residue frequencies and pairing preferences at protein-protein interfaces. Proteins 43: 89-102.
18. Jones S, Thornton JM, (1997) Analysis of protein-protein interaction sites using surface patches. J Mol Biol 272: 121-132.
19. Bahadur RP, Chakrabarti P, Rodier F, Janin J, (2003) Dissecting subunit interfaces in homodimeric proteins. Proteins 53: 708-719.
20. Chakrabarti P, Janin J, (2002) Dissecting protein-protein recognition sites. Proteins 47: 334-343.
21. Gong S, Park C, Choi H, Ko J, Jang I, et al. (2005) A protein domain interaction interface database: InterPare. BMC Bioinformatics 6: 207.
22. Tuncbag N, Kar G, Keskin O, Gursoy A, Nussinov R, (2009) A survey of available tools and web servers for analysis of protein-protein interactions and interfaces. Brief Bioinform 10: 217-232.
23. Kirkpatrick DG, Radke JD, (1985) A framework for computational morphology. Computational Geometry, Machine Intelligence and Pattern Recognition 2: 217-48.
24. Lo Conte L, Chothia C, Janin J, (1999) The atomic structure of protein-protein recognition sites. J Mol Biol 285: 2177-2198.
25. Janin J, Miller S, Chothia C, (1988) Surface, subunit interfaces and interior of oligomeric proteins. J Mol Biol 204: 155-164.
26. Carugo O, Argos P, (1997) Protein-protein crystal-packing contacts. Protein science 6: 2261-3.
27. Mintseris J, Weng Z, (2003) Atomic contact vectors in protein-protein recognition. Proteins 53: 629-639.
28. Block P, Paern J, Hullermeier E, Sanschagrin P, Sotriffer CA, et al. (2006) Physicochemical descriptors to discriminate protein-protein interactions in permanent and transient complexes selected by means of machine learning algorithms. Proteins 65: 607-622.
29. Ponstingl H, Kabir T, Thornton JM, (2003) Automatic inference of protein quaternary structure from crystals. Journal of Applied Crystallography 36: 1116-1122.
30. Bogan AA, Thorn KS, (1998) Anatomy of hot spots in protein interfaces. J Mol Biol 280: 1-9.
31. Liu Q, Li J, (2010) Propensity vectors of low-ASA residue pairs in the distinction of protein interactions. Proteins 78: 589-602.
32. Ponstingl H, Henrick K, Thornton JM, (2000) Discriminating between homodimeric and monomeric proteins in the crystalline state. Proteins 41: 47-57.
33. Krissinel E, Henrick K, (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372: 774-797.
34. Hubbard SJ, Thornton JM (1993) 'NACCESS', computer program. Technical report, Department of Biochemistry Molecular Biology, University College London.
35. Jain AN, (1996) Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities. Journal of Computer-Aided Molecular Design 10: 427-440.
36. Trott O, Olson AJ, (2010) AutoDock vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31: 455-461.
37. Gabriel KR, Sokal RR, (1969) A new statistical approach to geographic variation analysis. Systematic Zoology (Society of Systematic Biologists) 18: 259-270.
38. Matula DW, Sokal RR, (1980) Properties of gabriel graphs relevant to geographic variation research and clustering of points in the plane. Geogr Anal 12: 205-222.
39. Kim DS, Seo J, Kim D, Ryu J, Cho CH, (2006) Three-dimensional beta shapes. Computer-Aided Design 38: 1179-1191.
40. Edelsbrunner H, Mücke EP, (1994) Three-dimensional alpha shapes. ACM Trans Graph 13: 43-72.
41. Selvaraj S, Gromiha M, (2003) Role of hydrophobic clusters and long-range contact networks in the folding of (alpha/beta)8 barrel proteins. Biophys J 84: 1919-1925.
42. Wu S, Zhang Y, (2008) A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. Bioinformatics 24: 924-931.
43. Chen P, Li J, (2010) Prediction of protein long-range contacts using an ensemble of genetic algorithm classifiers with sequence profile centers. BMC Structural Biology 10: S2.
44. Barber BC, Dobkin DP, Huhdanpaa H, (1996) The quickhull algorithm for convex hulls. ACM Transactions on Mathematical Software 22: 469-483.
45. Tsai J, Taylor R, Chothia C, Gerstein M, (1999) The packing density in proteins: standard radii and volumes. J Mol Biol 290: 253-266.
46. Chang CC, Lin CJ (2001) LIBSVM: a library for support vector machines.