Use B-factor related features for accurate classification between protein binding interfaces and crystal packing contacts

BMC Bioinformatics

Volumn 15, Issue 16, 2014, Pages

  Liu, Qian ^a   Li, Zhenhua ^b   Li, Jinyan ^a  

^a UNIVERSITY OF TECHNOLOGY SYDNEY   (Australia)

^b NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMS; BINDING ENERGY; BINS; BIOCHEMISTRY; BIOINFORMATICS; CHAINS; COMPUTER AIDED DIAGNOSIS; CONTACTS (FLUID MECHANICS); PROTEINS; SURFACE CHEMISTRY;

BIOLOGICAL INTERACTIONS; BIOLOGICAL INTERFACE; CLASSIFICATION PERFORMANCE; DISTRIBUTION PROPERTY; PROTEIN INTERACTION; PROTEIN STRUCTURES; STRUCTURAL BIOINFORMATICS; VIBRATIONAL MOTIONS;

CLASSIFICATION (OF INFORMATION);

BINDING AFFINITY; CHEMICAL BINDING; CLASSIFICATION; CONTROLLED STUDY; CRYSTAL; EXPERIMENTAL MODEL; MOTION; PREDICTION; PROTEIN BINDING; QUANTITATIVE STUDY; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; HUMAN; METABOLISM; PROCEDURES; PROTEIN CONFORMATION; PROTEIN DATABASE; X RAY CRYSTALLOGRAPHY;

PROTEIN; PROTEIN BINDING;

COMPUTATIONAL BIOLOGY; CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; HUMANS; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEINS; SOFTWARE;

EID: 84961671506     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-15-S16-S3     Document Type: Article

References (30)

1. Tuncbag N, Kar G, Keskin O, Gursoy A, Nussinov R: A survey of available tools and web servers for analysis of protein-protein interactions and interfaces. Brief Bioinform. 2009, 10 (3): 217-232.
2. Valdar WSJ, Thornton JM: Conservation helps to identify biologically relevant crystal contacts. J Mol Biol. 2001, 313 (2): 399-416. 10.1006/jmbi.2001.5034.
3. Zhu H, Domingues FS, Sommer I, Lengauer T: NOXclass: prediction of protein-protein interaction types. BMC Bioinformatics. 2006, 7: 27-10.1186/1471-2105-7-27.
4. Bahadur RP, Chakrabarti P, Rodier F, Janin J: A dissection of specific and non-specific protein-protein interfaces. J Mol Biol. 2004, 336 (4): 943-955. 10.1016/j.jmb.2003.12.073.
5. Bahadur RP, Chakrabarti P, Rodier F, Janin J: Dissecting subunit interfaces in homodimeric proteins. Proteins. 2003, 53 (3): 708-719. 10.1002/prot.10461.
6. Janin J, Rodier F: Protein-protein interaction at crystal contacts. Proteins. 1995, 23 (4): 580-587. 10.1002/prot.340230413.
7. Janin J: Specific versus non-specific contacts in protein crystals. Nature Structural Biology. 1997, 4: 973-974. 10.1038/nsb1297-973.
8. Carugo O, Argos P: Protein-protein crystal-packing contacts. Protein science. 1997, 6 (10): 2261-2263.
9. Jones S, Thornton JM: Analysis of protein-protein interaction sites using surface patches. J Mol Biol. 1997, 272: 121-132. 10.1006/jmbi.1997.1234.
10. Lo Conte L, Chothia C, Janin J: The atomic structure of protein-protein recognition sites. J Mol Biol. 1999, 285 (5): 2177-2198. 10.1006/jmbi.1998.2439.
11. Mintseris J, Weng Z: Atomic contact vectors in protein-protein recognition. Proteins. 2003, 53 (3): 629-639. 10.1002/prot.10432.
12. Block P, Paern J, Hullermeier E, Sanschagrin P, Sotriffer CA, Klebe G: Physicochemical descriptors to discriminate protein-protein interactions in permanent and transient complexes selected by means of machine learning algorithms. Proteins. 2006, 65 (3): 607-622. 10.1002/prot.21104.
13. Liu Q, Kwoh CK, Hoi SCH: Beta Atomic Contacts: Identifying Critical Specific Contacts in Protein Binding Interfaces. PLoS ONE. 2013, 8 (4): e59737-10.1371/journal.pone.0059737.
14. Bernauer J, Bahadur RPP, Rodier F, Janin J, Poupon A: DiMoVo: a Voronoi tessellation-based method for discriminating crystallographic and biological protein-protein interactions. Bioinformatics. 2008, 24: 652-658. 10.1093/bioinformatics/btn022.
15. Liu Q, Li J: Propensity vectors of low-ASA residue pairs in the distinction of protein interactions. Proteins. 2010, 78: 589-602.
16. Ponstingl H, Kabir T, Thornton JM: Automatic inference of protein quaternary structure from crystals. Journal of Applied Crystallography. 2003, 36 (5): 1116-1122. 10.1107/S0021889803012421.
17. Duarte J, Srebniak A, Scharer M, Capitani G: Protein interface classification by evolutionary analysis. BMC Bioinformatics. 2012, 13: 334-10.1186/1471-2105-13-334.
18. Krissinel E, Henrick K: Inference of Macromolecular Assemblies from Crystalline State. J Mol Biol. 2007, 372 (3): 774-797. 10.1016/j.jmb.2007.05.022.
19. Cheng T, Li X, Li Y, Liu Z, Wang R: Comparative Assessment of Scoring Functions on a Diverse Test Set. J Chem Inf Model. 2009, 49 (4): 1079-1093. 10.1021/ci9000053.
20. Ponstingl H, Henrick K, Thornton JM: Discriminating between homodimeric and monomeric proteins in the crystalline state. Proteins. 2000, 41: 47-57. 10.1002/1097-0134(20001001)41:1<47::AID-PROT80>3.0.CO;2-8.
21. Yuan Z, Bailey TL, Teasdale RD: Prediction of protein B-factor profiles. Proteins: Struct, Funct, Bioinf. 2005, 58 (4): 905-912. 10.1002/prot.20375.
22. Parthasarathy S, Murthy MR: Analysis of temperature factor distribution in high-resolution protein structures. Protein Sci. 1997, 6 (12): 2561-2567.
23. Yuan Z, Zhao J, Wang ZX: Flexibility analysis of enzyme active sites by crystallographic temperature factors. Protein Eng. 2003, 16 (2): 109-114. 10.1093/proeng/gzg014.
24. Hubbard SJ, Thornton JM: 'NACCESS', computer program. Tech. rep., Department of Biochemistry Molecular Biology, University College London. 1993
25. Kirkpatrick DG, Radke JD: A framework for computational morphology. Computational Geometry, Machine Intelligence and Pattern Recognition. 1985, 2: 217-248.
26. Liu Q, Hoi SC, Kwoh CK, Wong L, Li J: Integrating water exclusion theory into beta contacts to predict binding free energy changes and binding hot spots. BMC Bioinformatics. 2014, 15: 57-10.1186/1471-2105-15-57.
27. Liu Q, Kwoh CK, Li J: Binding affinity prediction for protein-ligand complexes based on β contacts and B factor. Journal of Chemical Information and Modeling. 2013, 53 (11): 3076-3085. 10.1021/ci400450h.
28. Martin J: Benchmarking protein-protein interface predictions: Why you should care about protein size. Proteins: Structure, Function, and Bioinformatics. 2014, 82 (7): 1442-1452.
29. Henrick K, Thornton JM: PQS: a protein quaternary structure file server. Trends in Biochemical Sciences. 1998, 23 (9): 358-361. 10.1016/S0968-0004(98)01253-5.
30. Tarshis L, Proteau PJ, Kellogg BA, Sacchettini JC, Poulter C: Regulation of product chain length by isoprenyl diphosphate synthases. Proceedings of the National Academy of Sciences. 1996, 93 (26): 15018-15023. 10.1073/pnas.93.26.15018.