An integrated suite of fast docking algorithms

Proteins: Structure, Function and Bioinformatics

Volumn 78, Issue 15, 2010, Pages 3197-3204

  Mashiach, Efrat ^a   Schneidman Duhovny, Dina ^a   Peri, Aviyah ^a   Shavit, Yoli ^a   Nussinov, Ruth ^a,b   Wolfson, Haim J ^a  

^a TEL AVIV UNIVERSITY   (Israel)

^b SAIC FREDERICK INC   (United States)

Author keywords

Backbone flexibility; CAPRI; Docking refinement; Protein protein docking; Rigid body minimization; Side chain optimization

Indexed keywords

ADENOSINE DIPHOSPHATE RIBOSYLATION FACTOR 6; FORK HEAD ASSOCIATED DOMAIN STRUCTURE OF KIF13B; GUANOSINE TRIPHOSPHATE; LEUCINE ZIPPER PROTEIN; NUCLEAR PROTEIN; PROTEIN CENTAURIN ALPHA1; PROTEIN RND1; UNCLASSIFIED DRUG;

ALGORITHM; ARTICLE; BINDING SITE; BIOINFORMATICS; MOLECULAR DOCKING; PRIORITY JOURNAL; QUALITY CONTROL;

ALGORITHMS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; INTERNET; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPPING;

EID: 77957956522     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22790     Document Type: Article

References (33)

1. Lensink MF, Mendez R, Wodak SJ. Docking and scoring protein complexes: CAPRI 3rd Edition. Proteins 2007;69:704-718.
2. Janin J, Henrick K, Moult J, Eyck LT, Sternberg MJ, Vajda S, Vakser I, Wodak SJ. CAPRI: a Critical Assessment of PRedicted Interactions. Proteins 2003;52:2-9.
3. Janin J. The targets of CAPRI rounds 3-5. Proteins 2005;60:170-175.
4. Janin J. Sailing the route from Gaeta. Italy, to CAPRI. Proteins 2005;60:149.
5. Glaser F, Pupko T, Paz I, Bell RE, Bechor-Shental D, Martz E, BenTal N. ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 2003;19:163-164.
6. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990;215:403-410.
7. Shatsky M, Nussinov R, Wolfson HJ. A method for simultaneous alignment of multiple protein structures. Proteins 2004;56:143- 156.
8. Emekli U, Schneidman-Duhovny D, Wolfson HJ, Nussinov R, Haliloglu T. HingeProt: automated prediction of hinges in protein structures. Proteins 2008;70:1219-1227.
9. Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ. PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res 2005;33:W363-W367.
10. Duhovny D, Nussinov R, Wolfson HJ. Efficient unbound docking of rigid molecules. In: Guigó R, Gusfield D, editors. Lecture notes in computer science. Rome, Italy: Springer Berlin-Heidelberg; 2002. pp185-200.
11. Schneidman-Duhovny D, Nussinov R, Wolfson HJ. Automatic prediction of protein interactions with large scale motion. Proteins 2007;69:764-773.
12. Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ. Geometry-based flexible and symmetric protein docking. Proteins 2005;60:224-231.
13. Mashiach E, Nussinov R, Wolfson HJ. FiberDock: flexible inducedfit backbone refinement in molecular docking. Proteins 2010;78: 1503-1519.
14. Mashiach E, Schneidman-Duhovny D, Andrusier N, Nussinov R, Wolfson HJ. FireDock: a web server for flexible induced-fit backbone refinement in molecular docking. Nucleic Acids Res 2010; doi: 10.1093/nar/gkg373.
15. Andrusier N, Nussinov R, Wolfson HJ. FireDock: fast interaction refinement in molecular docking. Proteins 2007;69:139-159.
16. Schueler-Furman O, Wang C, Baker D. Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility. Proteins 2005;60:187-194.
17. Schueler-Furman O, Wang C, Bradley P, Misura K, Baker D. Progress in modeling of protein structures and interactions. Science 2005;310:638-642.
18. Mashiach E, Nassinov R, Wolfson HJ. FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking. Nucleic Acids Research 2010; doi: 10.1093/nar/gkq373.
19. Hwang H, Pierce B, Mintseris J, Janin J, Weng Z. Protein-protein docking benchmark version 3.0. Proteins 2008;73:705-709.
20. Leulliot N, Chaillet M, Durand D, Ulryck N, Blondeau K, van Tilbeurgh H. Structure of the yeast tRNA m7G methylation complex. Structure 2008;16:52-61.
21. Oinuma I, Katoh H, Harada A, Negishi M. Direct interaction of Rnd1 with Plexin-B1 regulates PDZ-RhoGEF-mediated Rho activation by Plexin-B1 and induces cell contraction in COS-7 cells. J Biol Chem 2003;278:25671-25677.
22. Tong Y, Hughes D, Placanica L, Buck M. When monomers are preferred: a strategy for the identification and disruption of weakly oligomerized proteins. Structure 2005;13:7-15.
23. Vikis HG, Li W, He Z, Guan KL. The semaphorin receptor plexin-B1 specifically interacts with active Rac in a ligand-dependent manner. Proc Natl Acad Sci USA 2000;97:12457-12462.
24. Micheelsen PO, Vevodova J, De Maria L, Ostergaard PR, Friis EP, Wilson K, Skjot M. Structural and mutational analyses of the interaction between the barley alpha-amylase/subtilisin inhibitor and the subtilisin savinase reveal a novel mode of inhibition. J Mol Biol 2008;380:681-690.
25. Pal GP, Kavounis CA, Jany KD, Tsernoglou D. The three-dimensional structure of the complex of proteinase K with its naturally occurring protein inhibitor, PKI3. FEBS Lett 1994;341:167-170.
26. Fiser A, Sali A. ModLoop: automated modeling of loops in protein structures. Bioinformatics 2003;19:2500-2501.
27. Isabet T, Montagnac G, Regazzoni K, Raynal B, El Khadali F, England P, Franco M, Chavrier P, Houdusse A, Menetrey J. The structural basis of Arf effector specificity: the crystal structure of ARF6 in a complex with JIP4. EMBO J 2009;28:2835-2845.
28. Venkateswarlu K, Hanada T, Chishti AH. Centaurin-alpha1 interacts directly with kinesin motor protein KIF13B. J Cell Sci 2005;118 (Part 11):2471-2484.
29. Bao R, Zhou CZ, Jiang C, Lin SX, Chi CW, Chen Y. The ternary structure of the double-headed arrowhead protease inhibitor API-A complexed with two trypsins reveals a novel reactive site conformation. J Biol Chem 2009;284:26676-26684.
30. Meenan NAG, Sharma A, Fleishman SJ, MacDonald C, Morel B, Boetzel R, Moore GR, Baker D, Kleanthous C. The structural and energetic basis for high selectivity in a high affinity protein-protein interaction. Proc Natl Acad Sci USA, in press.
31. Krachler AM, Sharma A, Regan L, Kleanthous C. Self-association of TPR-domains: natural and engineered. Proteins, in press.
32. Inbar Y, Schneidman-Duhovny D, Halperin I, Oron A, Nussinov R, Wolfson HJ. Approaching the CAPRI challenge with an efficient geometry-based docking. Proteins 2005;60:217-223.
33. Mendez R, Leplae R, Lensink MF, Wodak SJ. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins 2005;60:150-169.