Optimization of pyDock for the new CAPRI challenges: Docking of homology-based models, domain-domain assembly and protein-RNA binding

Proteins: Structure, Function and Bioinformatics

Volumn 78, Issue 15, 2010, Pages 3182-3188

  Pons, Carles ^a,b   Solernou, Albert ^a   Perez Cano, Laura ^a   Grosdidier, Solène ^a   Fernandez Recio, Juan ^a  

^a BARCELONA SUPERCOMPUTING CENTER   (Spain)

^b National Institute of Bioinformatics ^*  (Spain)

Author keywords

CAPRI; Complex structure; Protein protein docking; Protein RNA binding; pyDock

Indexed keywords

DIMER; RNA;

ARTICLE; MOLECULAR DOCKING; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; RNA BINDING;

ALGORITHMS; ANIMALS; CATTLE; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; ESCHERICHIA COLI PROTEINS; MODELS, CHEMICAL; MODELS, MOLECULAR; MONTE CARLO METHOD; PROTEIN BINDING; RNA; RNA-BINDING PROTEINS;

EID: 77957950490     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22773     Document Type: Article

References (34)

1. Chen R, Mintseris J, Janin J, Weng Z. A protein-protein docking benchmark. Proteins 2003;52:88-91.
2. Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z. Protein-protein docking benchmark 2.0: an update. Proteins 2005;60:214-216.
3. Hwang H, Pierce B, Mintseris J, Janin J, Weng Z. Protein-protein docking benchmark version 3.0. Proteins 2008;73:705-709.
4. Gao Y, Douguet D, Tovchigrechko A, Vakser IA. DOCKGROUND system of databases for protein recognition studies: unbound structures for docking. Proteins 2007;69:845-851.
5. Méndez R, Leplae R, De Maria L, Wodak SJ. Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins 2003;52:51-67.
6. Méndez 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.
7. Lensink MF, Méndez R, Wodak SJ. Docking and scoring protein complexes: CAPRI. Proteins 2007;69:704-718.
8. Fernández-Recio J, Totrov M, Abagyan R. Soft protein-protein docking in internal coordinates. Protein Sci 2002;11:280-291.
9. Fernández-Recio J, Totrov M, Abagyan R. ICM-DISCO docking by global energy optimization with fully flexible side-chains. Proteins 2003;52:113-117.
10. Fernández-Recio J, Abagyan R, Totrov M. Improving CAPRI predictions: optimized desolvation for rigid-body docking. Proteins 2005; 60:308-313.
11. Cheng TM, Blundell TL, Fernandez-Recio J. pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking. Proteins 2007;68:503-515.
12. Grosdidier S, Pons C, Solernou A, Fernández-Recio J. Prediction and scoring of docking poses with pyDock. Proteins 2007;69:852-858.
13. Chelliah V, Blundell TL, Fernández-Recio J. Efficient restraints for protein-protein docking by comparison of observed amino acid substitution patterns with those predicted from local environment. J Mol Biol 2006;357:1669-1682.
14. Cheng TMK, Blundell TL, Fernandez-Recio J. Structural assembly of two-domain proteins by rigid-body docking. BMC Bioinformatics 2008;9:441.
15. Gabb HA, Jackson RM, Sternberg MJ. Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol 1997;272:106-120.
16. Chen R, Weng Z. A novel shape complementarity scoring function for protein-protein docking. Proteins 2003;51:397-408.
17. Pons C, Grosdidier S, Solernou A, Pérez-Cano L, Fernández-Recio J. Present and future challenges and limitations in protein-protein docking. Proteins 2010;78:95-108.
18. Fernández-Recio J, Totrov M, Abagyan R. Identification of protein-protein interaction sites from docking energy landscapes. J Mol Biol 2004;335:843-865.
19. Fernandez-Recio J, Totrov M, Skorodumov C, Abagyan R. Optimal docking area: a new method for predicting protein-protein interaction sites. Proteins 2005;58:134-143.
20. Ponder JW, Richards FM. An efficient Newton-like method for molecular mechanics energy minimization of large molecules. J Comput Chem 1987;8:1016-1024.
21. Cornell WD, Cieplak P, Bayly CI, Gould IR, Mserz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 1995;117:5179-5197.
22. Still WC, Tempczyk A, Hawley RC, Hendrickson T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc 1990;112:6127-6129.
23. Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993;234:779-815.
24. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990;215:403-410.
25. Shen M, Sali A. Statistical potential for assessment and prediction of protein structures. Protein Sci 2006;15:2507-2524.
26. 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.
27. Bønsager BC, Nielsen PK, Abou Hachem M, Fukuda K, Praetorius-Ibba M, Svensson B. Mutational analysis of target enzyme recognition of the beta-trefoil fold barley alpha-amylase/subtilisin inhibitor. J Biol Chem 2005;280:14855-14864.
28. Micheelsen PO, Vévodová J, De Maria L, Ostergaard PR, Friis EP, Wilson K, Skjøt 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.
29. Bao R, Zhou C, Jiang C, Lin S, Chi C, 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. Li W, Hamill SJ, Hemmings AM, Moore GR, James R, Kleanthous C. Dual recognition and the role of specificity-determining residues in colicin E9 DNase-immunity protein interactions. Biochemistry 1998;37:11771-11779.
31. Keeble AH, Joachimiak LA, Maté MJ, Meenan N, Kirkpatrick N, Baker D, Kleanthous C. Experimental and computational analyses of the energetic basis for dual recognition of immunity proteins by colicin endonucleases. J Mol Biol 2008;379:745-759.
32. Grosdidier S, Fernández-Recio J. Identification of hot-spot residues in protein-protein interactions by computational docking. BMC Bioinformatics 2008;9:447.
33. 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 2010;107:10080-10085.
34. Krachler AM, Sharma A, Kleanthous C. Self-association of TPR-domains: Lessons learned from a designed, consensus-based TPR oligomer. Proteins 2010;78:2131-2143.