ISIS: Interaction sites identified from sequence

Bioinformatics

Volumn 23, Issue 2, 2007, Pages

  Ofran, Yanay ^a   Rost, Burkhard ^a  

^a Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONFERENCE PAPER; DATA ANALYSIS SOFTWARE; INFORMATION PROCESSING; PREDICTOR VARIABLE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEIN TARGETING; STRUCTURAL PROTEOMICS;

EID: 33846662784     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl303     Document Type: Conference Paper

References (38)

1. Aloy,P. and Russell,R.B. (2002) Interrogating protein interaction networks through structural biology. Proc. Natl Acad. Sci. USA, 99, 5896-5901.
2. Altschul,S. et al. (1997) Gapped Blast and PSI-Blast: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
3. Armon,A. et al. (2001) ConSurf an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J. Mol. Biol., 307, 447-463.
4. Bairoch,A. and Apweiler,R. (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res., 28, 45-48.
5. Berman,H.M. et al. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
6. Berman,H.M. et al. (2002) The Protein Data Bank. Acta Crystallogr. D Biol. Crystallogr., 58, 899-907.
7. Bernstein,F.C. et al. (1977) The Protein Data Bank: A computer-based archival file for macromolecular structures. J. Mol. Biol., 112, 535-542.
8. Bohr,H. et al. (1988) Protein secondary structure and homology by neural networks. FEBS Lett., 241, 223-228.
9. Bohr,H. et al. (1990) A novel approach to prediction of the 3-dimensional structures of protein backbones by neural networks. FEBS Lett., 261, 43-46.
10. Fariselli,P. et al. (2002) Prediction of protein-protein interaction sites in heterocomplexes with neural networks. Eur. J. Biochem., 269, 1356-1361.
11. Fernandez-Recio,J. et al. (2005) Optimal docking area: A new method for predicting protein-protein interaction sites. Proteins, A, 134-143.
12. Fischer,D. and Eisenberg,D. (1999) Finding families for genomic ORFans. Bioinformatics, 15, 759-762.
13. Gavin,A.C. et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature, 415, 141-147.
14. Giot,L. et al. (2003) A protein interaction map of Drosophila melanogaster. Science, 302, 1727-1736.
15. Ho,Y. et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature, 415, 180-183.
16. Jones,S. and Thornton,J.M. (1996) Principles of protein-protein interactions. Proc. Natl Acad. Sci. USA, 93, 13-20.
17. Jones,S. and Thornton,J.M. (1997) Prediction of protein-protein interaction sites using patch analysis. J. Mol. Biol., 272, 133-143.
18. Koike,A. and Takagi,T. (2004) Prediction of protein-protein interaction sites using support vector machines. Protein Eng. Des. Sel., 17, 165-173.
19. Li,S. et al. (2004) A map of the interactome network of the metazoan C. elegans. Science, 303, 540-543.
20. Mika,S. and Rost,B. (2006) (in press).
21. Nair,R. and Rost,B. (2002) Sequence conserved for subcellular localization. Prot. Sci., 11, 2836-2847.
22. Neuvirth,H. et al. (2004) ProMate: A structure based prediction program to identify the location of protein-protein binding sites. J. Mol. Blol., 338, 181-199.
23. Ofran,Y. and Rost,B. (2003a) Analysing six types of protein-protein interfaces. J. Mol. Biol., 325, 377-387.
24. Ofran,Y. and Rost,B. (2003b) Predicted protein-protein interaction sites from local sequence information. FEBS Lett., 544, 236-239.
25. Pazos,F. and Valencia,A. (2002) In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins, 47, 219-227.
26. Qian,N. and Sejnowski,T.J. (1988) Predicting the secondary structure of globular proteins using neural network models. J. Mol. Biol., 202, 865-884.
27. Res,I. et al. (2005) An evolution based classifier for prediction of protein interfaces without using protein structures. Bioinformatics, 21, 2496-2501.
28. Rost,B. (1999) Twilight zone of protein sequence alignments. Prot. Eng., 12, 85-94.
29. Rost,B. (2002a) Enzyme function less conserved than anticipated. J. Mol. Biol., 318, 595-608.
30. Rost,B. (2002b) Prediction in 1D: Secondary structure, membrane helices, and accessibility. In Bourne,P. and Weissig,H. (eds), Structural Bioinformatics. John Wiley. pp. 559-588.
31. Rost,B. (2004) How to use protein 1D structure predicted by PROFphd. Meth. Mol. Biol.
32. Rost,B. and Sander,C. (1993) Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol., 232, 584-599.
33. Rost,B. et al. (2003) Automatic prediction of protein function. Cell Mol. Life Sci., 60, 2637-2650.
34. Sander,C. and Schneider,R. (1991) Database of homology-derived structures and the structural meaning of sequence alignment. Proteins, 9, 96-68.
35. Schneider,R. and Sander,C. (1996) The HSSP database of protein structure-sequence alignments. Nucleic Acids Res., 24, 201-205.
36. Uetz,P. et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403, 623-627.
37. Wang,B. et al. (2005) Predicting protein interaction sites from residue spatial sequence profile and evolution rate. FEBS Lett, 580, 380-384.
38. Wodak,S.J. and Mendez,R. (2004) Prediction of protein-protein interactions: The CAPRI experiment, its evaluation and implications. Curr. Opin. Struct. Biol., 14, 242-249.