Predicting protein-protein interactions using first principle methods and statistical scoring

ISB 2010 Proceedings - International Symposium on Biocomputing

Volumn , Issue , 2010, Pages

  Pradhan, Meeta P ^a   Gandra, Premchand ^a   Palakal, Mathew J ^a  

^a INDIANA UNIVERSITY   (United States)

Author keywords

Patch residue; Protein protein interaction; Sliding window

Indexed keywords

DATA SETS; FIRST PRINCIPLE METHOD; FIRST-PRINCIPLES; NOVEL TECHNIQUES; PHYSICOCHEMICAL PROPERTY; PREDICTION MODEL; PROTEIN INTERACTION; PROTEIN-PROTEIN INTERACTIONS; SLIDING WINDOW; SLIDING WINDOW ALGORITHMS;

ABSTRACTING; CHEMICAL PROPERTIES; FORECASTING; MATHEMATICAL MODELS; SOOT BLOWERS;

PROTEINS;

EID: 77951603542     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/1722024.1722038     Document Type: Conference Paper

References (25)

1. Antony A, Bassetty S, Haranto S, Palakal M. Computational approach to biological validation of protein-protein interactions discovered using literature mining. ACM Symposium on Applies Computing, Fortaleza, Brasil, 2008.
2. Bahadur RP and Zacharias M. The interface of protein-protein complexes: Analysis of contacts and prediction of interactions. Cell. Mol. Life. Sci. 2008:1059-1072.
3. Bordner A and Abagyan R. Statistical analysis and prediction of protein-protein interfaces. PROTEINS: Structure, Function and Genetics 2005; 60:353-366. (Pubitemid 41061632)
4. Bradford JR, Needham CJ, Bulpitt AJ, Westhead DR. J. Mol. Biol. 2006; 362:365-386.
5. Deng M, Mehta S, Sun F and Chen T. Inferring Domain-Domain interactions from Protein-protein interaction. Genome Res. 2002; 12(10):1540-1548. (Pubitemid 35175092)
6. Eisenberg D, Weiss RM, Terwilliger TC. The helical hydrophobic moments and protein structure. Faraday Symp. Chem. Soc. 1982; 17:109-120.
7. Finn RD, Marshall M, and Bateman A. iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions. Bioinformatics 2005; 21 (3):410-412 (Pubitemid 40246619)
8. Finn RD, Tate J, Mistry J, Coggill PC, Sammut JS, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL and Bateman A. The Pfam protein families database. Nucleic Acids Research 2008. Database issue 36:D281-D288 [16]
9. Finn RD, Tate J, Mistry J, Coggill PC, Sammut JS, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A. The Pfam protein families' database. Nucleic Acid Research 2008.
10. Gallet X, Charloteaux B, Thomas A and Brasseur R. A fast method to predict protein protein interaction sites from sequences. J.Mol.Biol. 2000; 302:917-926.
11. Gandra P, Pradhan MP and Palakal MJ . Biomedical Association Mining and Validation [Accepted for ISB 2010]. [12] http://mint.bio.uniroma2.it/mint/
12. http://bond.unleashedinformatics.com/
13. http://www.hprd.org/
14. Huang C, Morcos F, Kanaan SP, Wuchty S, Chen DZ and Izaguirre JA. Predicting protein-protein interactions from protein domains using a set cover approach. IEEE/ACM Transactions on computational biology and bioinformatics 2007; 4(1):78-87. (Pubitemid 46379755)
15. Jones S and Thornton JM. Prediction of protein-protein interaction sites using patch analysis. J. Mol. Biol 1997; 272:133-143. (Pubitemid 27395543)
16. Keskin O, Gursoy A, Ma B, and Nussinov R. Principles of protein-protein interactions: What are the preferred ways for proteins to interact? Chem. Rev. 2008; 108(4): 1225-1244. (Pubitemid 351638814)
17. Lu H and Skolnick J. A distance-dependent atomic knowledge-based potential for improved protein structure selection. PROTEINS: Structure, Function and Genetics 2001; 44:223-232. (Pubitemid 32702231)
18. Lu H, Lu L and Skolnick J. Development of unified statistical potentials describing protein-protein interactions. J. Biophys. 2003; 84:1895-1901. (Pubitemid 36322951)
19. Metacore [www.genego.com].
20. Orfan Y. And Rost B. Analyzing six types of protein-protein interfaces. J. Mol. Biol. 2003; 325: 377-387.
21. Ortutay C and Vihinen M. Identification of candidate disease genes by integrating gene ontologies and protein-interaction networks: case study of primary immunodeficiencies. Nucleic Acid Research 2009; 37(2):622-628.
22. Pandey G, Steinbach M, Gupta R, Garg T and Kumar V. ACM 2007; 12-15
23. Skolnick J, Kolinski A and Ortiz. Derivation of protein-specific pair potentials based on weak sequence fragment similarity. PROTEINS: Structure, Function and Genetics 2000; 38:3-16.
24. Singh R, Xu J and Berger B. Struct2Net: Integrating structure into protein-protein interaction prediction. Pac. Symp. Biocomp. 2006; 11:403-414.
25. Zhang C and Kim SH. Environment-dependent residue contact energies for proteins. PNAS 2000; 97(6):2550-2555.