PRUNE and PROBE - Two modular web services for protein-protein docking

Nucleic Acids Research

Volumn 39, Issue SUPPL. 2, 2011, Pages

  Mitra, Pralay ^a   Pal, Debnath ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; CLIENT SERVER APPLICATION; COMPUTER INTERFACE; INFORMATION PROCESSING; INFORMATION RETRIEVAL; INTERNET; MOLECULAR DOCKING; PRIORITY JOURNAL; PROTEIN STRUCTURE; REGRESSION ANALYSIS;

ALGORITHMS; INTERNET; MODELS, MOLECULAR; MULTIPROTEIN COMPLEXES; PROTEIN INTERACTION MAPPING; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 79959948212     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr317     Document Type: Article

References (31)

1. Ritchie, D.W. (2008) Recent progress and future directions in protein-protein docking. Curr. Protein Pept. Sci., 9, 1-15.
2. Macindoe, G., Mavridis, L., Venkatraman, V., Devignes, M.D. and Ritchie, D.W. (2010) HexServer: an FFT-based protein docking server powered by graphics processors. Nucleic Acids Res., 38, W445-W449.
3. Mashiach, E., Schneidman-Duhovny, D., Andrusier, N., Nussinov, R. and Wolfson, H.J. (2008) FireDock: a web server for fast interaction refinement in molecular docking. Nucleic Acids Res., 36, W229-W232.
4. Lyskov, S. and Gray, J.J. (2008) The RosettaDock server for local protein-protein docking. Nucleic Acids Res., 36, W233-W238.
5. Tovchigrechko, A. and Vakser, I.A. (2006) GRAMM-X public web server for protein-protein docking. Nucleic Acids Res., 34, W310-W314. (Pubitemid 44529784)
6. Schneidman-Duhovny, D., Inbar, Y., Nussinov, R. and Wolfson, H.J. (2005) PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res., 33, W363-W367. (Pubitemid 44529944)
7. Comeau, S.R., Gatchell, D.W., Vajda, S. and Camacho, C.J. (2004) ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics, 20, 45-50. (Pubitemid 38088339)
8. Chen, R., Li, L. and Weng, Z. (2003) ZDOCK: an initial-stage protein-docking algorithm. Proteins, 52, 80-87. (Pubitemid 36648854)
9. Neuvirth, H., Raz, R. and Schreiber, G. (2004) ProMate: a structure based prediction program to identify the location of protein-protein binding sites. J. Mol. Biol., 338, 181-199. (Pubitemid 38429796)
10. Mashiach, E., Nussinov, R. and Wolfson, H.J. (2010) FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking. Nucleic Acids Res., 38, W457-W461.
11. Fischer, D., Lin, S.L., Wolfson, H.L. and Nussinov, R. (1995) A geometry-based suite of molecular docking processes. J. Mol. Biol., 248, 459-477.
12. Goodsell, D.S. and Olson, A.J. (1990) Automated docking of substrates to proteins by simulated annealing. Proteins, 8, 195-202. (Pubitemid 20363304)
13. Mitra, P. (2010) Algorithmic approaches for protein-protein docking and quaternary structure inference. PhD Thesis, Indian Institute of Science, Bangalore.
14. Andrusier, N., Nussinov, R. and Wolfson, H.J. (2007) FireDock: fast interaction refinement in molecular docking. Proteins, 69, 139-159. (Pubitemid 47339146)
15. Gabb, H.A., Jackson, R.M. and Sternberg, M.J. (1997) Modelling protein docking using shape complementarity, electrostatics and biochemical information. J. Mol. Biol., 272, 106-120. (Pubitemid 27395541)
16. Mitra, P. and Pal, D. (2010) New measures for estimating surface complementarity and packing at protein-protein interfaces. FEBS Lett., 584, 1163-1168.
17. Mitra, P. and Pal, D. (2011) Using correlated parameters for improved ranking of protein-protein docking decoys. J. Comput. Chem., 32, 787-796.
18. Lensink, M.F. and Wodak, S.J. (2010) Docking and scoring protein interactions: CAPRI 2009. Proteins, 78, 3073-3084.
19. Liang, S., Meroueh, S.O., Wang, G., Qiu, C. and Zhou, Y. (2009) Consensus scoring for enriching near-native structures from protein-protein docking decoys. Proteins, 75, 397-403.
20. Pierce, B. and Weng, Z. (2007) ZRANK: reranking protein docking predictions with an optimized energy function. Proteins, 67, 1078-1086. (Pubitemid 46753952)
21. Liang, S., Wang, G. and Zhou, Y. (2009) Refining near-native protein-protein docking decoys by local resampling and energy minimization. Proteins, 76, 309-316.
22. Pierce, B. and Weng, Z. (2008) A combination of rescoring and refinement significantly improves protein docking performance. Proteins, 72, 270-279. (Pubitemid 351809165)
23. Lee, B. and Richards, F.M. (1971) The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol., 55, 379-400.
24. Mintseris, J., Wiehe, K., Pierce, B., Anderson, R., Chen, R., Janin, J. and Weng, Z. (2005) Protein-protein docking benchmark 2.0: an update. Proteins, 60, 214-216. (Pubitemid 40934889)
25. Mendez, R., Leplae, R., De Maria, L. and Wodak, S.J. (2003) Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins, 52, 51-67. (Pubitemid 36648851)
26. Hubbard, S. and Thornton, J.M. (1993) NACCESS 2.1.1 ed. Department of Biochemistry and Molecular Biology, University College, London.
27. Bernauer, J., Aze, J., Janin, J. and Poupon, A. (2007) A new protein-protein docking scoring function based on interface residue properties. Bioinformatics, 23, 555-562. (Pubitemid 46522588)
28. Hwang, H., Vreven, T., Janin, J. and Weng, Z. (2010) Protein-protein docking benchmark version 4.0. Proteins, 78, 3111-3114.
29. Hwang, H., Pierce, B., Mintseris, J., Janin, J. and Weng, Z. (2008) Protein-protein docking benchmark version 3.0. Proteins, 73, 705-709. (Pubitemid 352788651)
30. Feliu, E. and Oliva, B. (2010) How different from random are docking predictions when ranked by scoring functions? Proteins, 78, 3376-3385.
31. Kozakov, D., Hall, D.R., Beglov, D., Brenke, R., Comeau, S.R., Shen, Y., Li, K., Zheng, J., Vakili, P., Paschalidis, I. et al. (2010) Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19. Proteins, 78, 3124-3130.