ReplicOpter: A replicate optimizer for flexible docking

Proteins: Structure, Function and Bioinformatics

Volumn 78, Issue 15, 2010, Pages 3156-3165

  Demerdash, Omar N A ^a   Buyan, Amanda ^a   Mitchell, Julie C ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

Aromatic interactions; Homology models; Local optimization; Protein deformation; Protein docking

Indexed keywords

ARTICLE; HYDROGEN BOND; MOLECULAR DOCKING; PRIORITY JOURNAL; PROTEIN STRUCTURE; QUALITY CONTROL; STATIC ELECTRICITY;

ALGORITHMS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPPING; PROTEINS; SOFTWARE;

EID: 77957947153     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22811     Document Type: Article

References (59)

1. 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.
2. Mendez 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.
3. Chen R, Li L, Weng Z. ZDOCK: an initial-stage protein-docking algorithm. Proteins 2003;52:80-87.
4. Chen R, Weng Z. Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins 2002;47:281-294.
5. Chen R, Weng Z. A novel shape complementarity scoring function for protein-protein docking. Proteins 2003;51:397-408.
6. Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ. Geometry-based flexible and symmetric protein docking. Proteins 2005; 60:224-231.
7. Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ. Patch-Dock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res 2005;33:W363-367.
8. Pierce B, Tong W, Weng Z. M-ZDOCK: a grid-based approach for Cn symmetric multimer docking. Bioinformatics 2005;21: 1472-1478.
9. Cho KI, Lee K, Lee KH, Kim D, Lee D. Specificity of molecular interactions in transient protein-protein interaction interfaces. Proteins 2006;65:593-606.
10. Bonvin AM. Flexible protein-protein docking. Curr Opin Struct Biol 2006;16:194-200.
11. Comeau SR, Gatchell DW, Vajda S, Camacho CJ. ClusPro: An automated docking and discrimination method for the prediction of protein complexes. Bioinformatics 2004;20:45-50.
12. Kozakov D, Clodfelter KH, Vajda S, Camacho CJ. Optimal clustering for detecting near-native conformations in protein docking. Biophys J 2005;89:867-875.
13. Andrusier N, Nussinov R, Wolfson HJ. FireDock: Fast interaction refinement in molecular docking. Proteins 2007;69:139-159.
14. Bastard K, Prevost C, Zacharias M. Accounting for loop flexibility during protein-protein docking. Proteins 2006;62:956-969.
15. Bastard K, Thureau A, Lavery R, Prevost C. Docking macromolecules with flexible segments. J Comput Chem 2003;24: 1910-1920.
16. Cavasotto CN, Kovacs JA, Abagyan RA. Representing receptor flexibility in ligand docking through relevant normal modes. J Am Chem Soc 2005;127:9632-9640.
17. Chaudhury S, Gray JJ. Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles. J Mol Biol 2008;381:1068-1087.
18. Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 2003;331:281-299.
19. Kovacs J, Cavasotto CN, Abagyan RA. Receptor conformational sampling through normal mode analysis and its application to virtual screening. Biophys J 2005;88:334A-334A.
20. May A, Zacharias M. Protein-protein docking in CAPRI using ATTRACT to account for global and local flexibility. Proteins 2007;69:774-780.
21. Schneidman-Duhovny D, Nussinov R, Wolfson HJ. Automatic prediction of protein interactions with large scale motion. Proteins 2007;69:764-773.
22. Shen Y, Paschalidis IC, Vakili P, Vajda S. Protein docking by the underestimation of free energy funnels in the space of encounter complexes. PLoS Comput Biol 2008;4:e1000191, doi: 10.1371/journal.pcbi.1000191.
23. Wang C, Bradley P, Baker D. Protein-protein docking with backbone flexibility. J Mol Biol 2007;373:503-519.
24. May A, Zacharias M. Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking. Proteins 2008;70:794-809.
25. Weeks JD, Chandler D, Andersen HC. Role of Repulsive Forces in Determining Equilibrium Structure of Simple Liquids. J Chem Phys 1971;54:5237.
26. Zhang C, Vasmatzis G, Cornette JL, DeLisi C. Determination of atomic desolvation energies from the structures of crystallized proteins. J Mol Biol 1997;267:707-726.
27. Mayo SL, Olafson BD, Goddard W, III. DREIDING: A generic force field for molecular simulations. J Phys Chem 1990;94:8897-8909.
28. Hastie T, Tibshirani R, Friedman J. The Elements of Statistical Learning. New York: Springer; 2001.
29. Eads D. hcluster: Hierarchical clustering for SciPy; 2008. http://code.google.com/p/scipy-cluster/
30. Johnson MG. Nonlinear optimization using the algorithm of Hooke and Jeeves; 1994. http://www.netlib.org/opt/hooke.c
31. Desmet J, Demaeyer M, Hazes B, Lasters I. The Dead-End Elimination Theorem and Its Use in Protein Side-Chain Positioning. Nature 1992;356:539-542.
32. Holm L, Kaariainen S, Rosenstrom P, Schenkel A. Searching protein structure databases with DaliLite v.3. Bioinformatics 2008;24:2780-2781.
33. Zhang Y, Skolnick J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 2005;33:2302-2309.
34. Sali A, Blundell TL. Comparative Protein Modeling by Satisfaction of Spatial Restraints. J Mol Biol 1993;234:779-815.
35. Mackerell AD, Feig M, Brooks CL. Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem 2004;25:1400-1415.
36. MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 1998;102:3586-3616.
37. Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res 2004;32:W665-667.
38. Li H, Robertson AD, Jensen JH. Very fast empirical prediction and rationalization of protein pKa values. Proteins 2005;61:704-721.
39. Yuki H, Tanaka Y, Hata M, Ishikawa H, Neya S, Hoshino T. Implementation of pi-pi interactions in molecular dynamics simulation. J Comput Chem 2007;28:1091-1099.
40. Minoux H, Chipot C. Cation-pi interactions in proteins: can simple models provide an accurate description? J Am Chem Soc 1999;121:10366-10372.
41. Gilis D, Biot C, Buisine E, Dehouck Y, Rooman M. Development of novel statistical potentials describing cation-pi interactions in proteins and comparison with semiempirical and quantum chemistry approaches. J Chem Inf Model 2006;46:884-893.
42. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, Schulten K. Scalable molecular dynamics with NAMD. J Comput Chem 2005;26:1781-1802.
43. Krebs W, Alexandrov V, Wilson C, Echols N, HY Y, Gerstein M. Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic. Proteins 2002;48:682-695.
44. Tama F, Gadea FX, Marques O, Sanejouand YH. Building-block approach for determining low-frequency normal modes of macromolecules. Proteins 2000;41:1-7.
45. Li G, Cui Q. A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to Ca(2+)-ATPase. Biophys J 2002;83:2457-2474.
46. Durand P, Trinquier G, Sanejouand YH. New Approach for Determining Low-Frequency Normal-Modes in Macromolecules. Biopolymers 1994;34:759-771.
47. 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.
48. Vajda S, Kozakov D. Convergence and combination of methods in protein-protein docking. Curr Opin Struct Biol 2009;19:164-170.
49. Ritchie DW, Kemp GJ. Protein docking using spherical polar Fourier correlations. Proteins 2000;39:178-194.
50. 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.
51. Sheinerman FB, Norel R, Honig B. Electrostatic aspects of proteinprotein interactions. Curr Opin Struct Biol 2000;10:153-159.
52. McCoy AJ, Epa VC, Colman PM. Electrostatic complementarity at protein/protein interfaces. J Mol Biol 1997;268:570-584.
53. 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.
54. Kleanthous C, Kuhlmann UC, Pommer AJ, Ferguson N, Radford SE, Moore GR, James R, Hemmings AM. Structural and mechanistic basis of immunity toward endonuclease colicins. Nat Struct Biol 1999;6:243-252.
55. Keeble AH, Joachimiak LA, Mate 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.
56. Li W, Keeble AH, Giffard C, James R, Moore GR, Kleanthous C. Highly discriminating protein-protein interaction specificities in the context of a conserved binding energy hotspot. J Mol Biol 2004;337:743-759.
57. 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.
58. Hwang H, Pierce B, Mintseris J, Janin J, Weng Z. Protein-protein docking benchmark version 3.0. Proteins 2008;73:705-709.
59. DeLano W. PyMol: DeLano Scientific LLC; 2008.