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InterPare Related Papers
Following papers are related with three methods used in InterPare
- Geometric distance method (PSIMAP method)
- 2001 : Generating protein interaction maps from incomplete data : Application to fold assignment Lappe M, Park J, Niggemann O, Holm L. Bioinformatics. 2001; 17 Suppl 1:S149-56.
- 2001 : Conservation of protein interaction network in evolution. Park J, Bolser D. Genome Inform Ser Workshop Genome Inform. 2001;12:135-40.
- 2003 : Visualization and graph-theoretic analysis of a large-scale protein structural interactome. Bolser D, Dafas P, Harrington R, Park J, Schroeder M. BMC Bioinformatics. 2003 Oct 08;4(1):45.
- 2004 : Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP). Kim WK, Bolser DM, Park JH. Bioinformatics. 2004 Feb 5.
- 2004 : Using convex hulls to extract interaction interfaces from known structures. Panos Dafas, Dan Bolser, Jacek Gomoluch, Jong Park, and Michael Schroeder. Bioinformatics 2004 20: 1486-1490.
- 2005 : PSIbase: a database of Protein Structural Interactome map (PSIMAP). Gong S, Yoon G, Jang I, Bolser D, Dafas P, Schroeder M, Choi H, Cho Y, Han K, Lee S, Choi H, Lappe M, Holm L, Kim S, Oh D, Bhak J. Bioinformatics. 2005 Mar 3
- Solvent Accessible Surface Area (ASA)
Lee B, Richards FM: The Interpretation of Protein Structures: Estimation of Static Accessibility. J Mol Biol 1971, 55:379-400.
Hubbard, SJ, Thornton, JM: NACCESS. Department of Biochemistry and Molecular Biology, University College, 1993, London.
Miller S, Janin J, Lesk AM, Chothia C: Interior and surface of monomeric proteins. J Mol Biol 1987, 196:641-656.
Jones S, Thornton JM: Principles of protein-protein interactions. Proc Natl Acad Sci 1996, 93: 13-20.
Jones S, Thornton JM: Analysis of Protein-protein interaction sites using surface patches. J Mol Biol 1997, 272:121-132.
Jones S, Marin A, Thornton JM: Protein domain interfaces: characterization and comparison with oligomeric protein interfaces. Protein Engineering 2000, 13:77-82.
- Voronoi diagram
Ban YEA, Edelsbrunner H, Rudolph J: Interface surfaces for protein-protein complexes. In Proceedings of the Research in Computational Molecular Biology, San Diego: March 2004; 27-31.
Richards FM: The interpretation of protein structures: total volume, group volume distributions and packing density. J Mol Biol 1974, 82:1-14.
Richards FM: Area, volumes, packing and protein structures. Ann Rev Biophys Bioeng 1977, 6:151-176.
Varshney A, Brooks F, Richardson D: Defining, Computing, and Visualizing Molecular Interfaces. IEEE Visualization 1995, 95:36-43.
Halperin, D, Overmars, MH: Spheres, Molecules, and Hidden Surface Removal. The Proceedings of the 10th Annual ACM Symposium of Computaitional Geometry, 1994, 113-122.
Dwyer, RA: Higher-Dimensional Voronoi Diagrams in Linear Expected Time. The Proceedings of the 5th Annual ACM Symposium on Computational Geometry, 1989, 326-333.
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