PROCOS: Computational analysis of protein-protein complexes

Journal of Computational Chemistry

Volumn 32, Issue 12, 2011, Pages 2575-2586

  Fink, Florian ^a   Hochrein, Jochen ^a   Wolowski, Vincent ^b   Merkl, Rainer ^a   Gronwald, Wolfram ^a  

^a UNIVERSITY OF REGENSBURG   (Germany)

^b UNIVERSITY OF HAGEN   (Germany)

Author keywords

docking; protein protein complex; reranking; scoring; support vector machine

Indexed keywords

AUTOMATED METHODS; BINARY TARGETS; COMPLEX ANALYSIS; COMPLEX STRUCTURE; COMPUTATIONAL ANALYSIS; EXPECTED VALUES; HIGH PROBABILITY; LARGE DATABASE; NATIVE COMPLEX; PROTEIN-PROTEIN COMPLEXES; PROTEIN-PROTEIN DOCKING; RE-RANKING; SCORING; SCORING SCHEMES; SCORING SYSTEMS; SUPPORT VECTOR;

DOCKING; PROBABILITY; SUPPORT VECTOR MACHINES;

PROTEINS;

MULTIPROTEIN COMPLEX; PROTEIN;

ALGORITHM; ARTICLE; ARTIFICIAL INTELLIGENCE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM; METHODOLOGY; PROTEIN ANALYSIS; PROTEIN BINDING;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; COMPUTATIONAL BIOLOGY; MODELS, MOLECULAR; MULTIPROTEIN COMPLEXES; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTEINS;

EID: 79959738645     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21837     Document Type: Article

References (37)

1. Berman, H. M.,;, Westbrook, J.,;, Feng, Z.,;, Gilliland, G.,;, Bhat, T. N.,;, Weissig, H.,;, Shindyalov, I. N.,;, Bourne, P. E., Nucleic Acids Res 2000, 28, 235.
2. Aloy, P.,;, Russel, R. B., Nat Biotech 2004, 22, 1317.
3. Ritchie, D. W., Curr Prot Pep Sci 2008, 9, 1.
4. Janin, J.,;, Wodak, S., Structure 2007, 15, 755.
5. Lensink, M. F.,;, Méndez, R.,;, Wodak, S., Proteins 2007, 69, 704.
6. Katchalski-Katzir, E.,;, Shariv, I.,;, Eisenstein, M.,;, Friesem, A. A.,;, Aflalo, C.,;, Vakser, I. A., Proc Natl Acad Sci USA 1992, 89, 2195.
7. Walls, P. H.,;, Sternberg, M. J., J Mol Biol 1992, 228, 277.
8. Gabb, H. A.,;, Jackson, R. M.,;, Sternberg, M. J., J Mol Biol 1997, 272, 106.
9. Mandell, J. G.,;, Roberts, V. A.,;, Pique, M. E.,;, Kotlovyi, V.,;, Mitchell, J. C.,;, Nelson, E.,;, Tsigelny, I.,;, TenEyck, L. F., Protein Eng 2001, 14, 105.
10. Heifetz, A.,;, Katchalski-Katzir, E.,;, Eisenstein, M., Protein Sci 2002, 11, 571.
11. Meyer, M.,;, Wilson, P.,;, Schomburg, D., J Mol Biol 1996, 264, 199.
12. Moont, G.,;, Gabb, H. A.,;, Sternberg, M. J., Proteins 1999, 35, 364.
13. Zhang, C.,;, Liu, S.,;, Zhou, H.,;, Zhou, Y., Protein Sci 2004, 13, 400.
14. Fernández-Recio, J.,;, Totrov, M.,;, Skorodumov, C.,;, Abagyan, R., Proteins 2005, 58, 134.
15. Camacho, C. J.,;, Gatchell, D. W.,;, Kimura, S. R.,;, Vajda, S., Proteins 2000, 40, 525.
16. Murphy, J.,;, Gatchell, D. W.,;, Prasad, J. C.,;, Vajda, S., Proteins 2003, 53, 840.
17. Li, C. H.,;, Ma, X. H.,;, Shen, L. Z.,;, Chang, S.,;, Chen, W. Z.,;, Wang, C. X., Biophys Chem 2007, 129, 1.
18. Müller, W.,;, Sticht, H., Proteins 2007, 67, 98.
19. Martin, O.,;, Schomburg, D., Proteins 2008, 70, 1367.
20. Dominguez, C.,;, Boelens, R.,;, Bonvin, A. M. J. J., J Am Chem Soc 2003, 125, 1731.
21. Kastritis, P. L.,;, Bonvin, A. M. J. J., J Proteome Res 2010, 9, 2216.
22. Cornfield, J., Biometrics 1969, 25, 617.
23. Mintz, S.,;, Shulman-Peleg, A.,;, Wolfson, H. J.,;, Nussinov, R., Proteins 2005, 61, 6.
24. Wolowski, V. R., Computational analysis of protein-protein complexes related to knowledge based predictions of interaction, Master thesis, Department of Computer Science, University of Hagen, German, 2008.
25. Capri homepage. Available at.
26. Ezkurdia, I.,;, Bartoli, L.,;, Fariselli, P.,;, Casadio, R.,;, Valencia, A.,;, Tress, M. L., Brief Bioinform 2009, 10, 233.
27. Word, J. M.,;, Lovell, S. C.,;, Richardson, J. S.,;, Richardson, D. C., J Mol Biol 1999, 285, 1735.
28. Brünger, A. T.,;, Adams, P. D.,;, Clore, G. M.,;, DeLano, W. L.,;, Gros, P.,;, Grossekunstleve, R. W.,;, Jiang, J. S.,;, Kuszewski, J.,;, Nilges, M.,;, Pannu, N. S.,;, Read, R. J.,;, Rice, L. M.,;, Simonson, T.,;, Warren, G. L., Acta Cryst D 1998, 54, 905.
29. deVries, S. J.,;, vanDijk, A. D. J.,;, Krzeminski, M.,;, vanDijk, M.,;, Thureau, A.,;, Hsu, V.,;, Wassenaar, T.,;, Bonvin, A. M. J. J., Proteins 2007, 69, 726.
30. Chang, C. C.,;, Lin, C. J., 2001.
31. Pierce, B.,;, Weng, Z., Proteins 2007, 67, 1078.
32. Yang, Y.,;, Zhou, Y., Proteins 2008, 72, 793.
33. Mintseris, J.,;, Wiehe, K.,;, Pierce, B.,;, Anderson, R.,;, Chen, R.,;, Janin, J.,;, Weng, Z., Proteins 2005, 60, 214.
34. Chen, R.,;, Mintseris, J.,;, Janin, J.,;, Weng, Z., Proteins 2003, 52, 88.
35. Liu, S.,;, Gao, Y.,;, Vakser, I. A., Bioinformatics 2008, 24, 2634.
36. Tovchigrechko, A.,;, Vakser, I. A., Proteins 2005, 60, 296.
37. Gray, J. J.,;, Moughon, S.,;, Wang, C.,;, Schueler-Furman, O.,;, Kuhlman, B.,;, Rohl, C. A.,;, Baker, D., J Mol Biol 2003, 331, 281.