Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking

Proteins: Structure, Function and Genetics

Volumn 66, Issue 2, 2007, Pages 399-421

  Huang, Sheng You ^a   Zou, Xiaoqin ^a  

^a UNIVERSITY OF MISSOURI   (United States)

Author keywords

Ligand protein interactions; Molecular docking; Protein ensemble; Protein flexibility; Structure based drug design

Indexed keywords

PROTEINASE;

ALGORITHM; ARTICLE; CRYSTAL STRUCTURE; MOLECULAR DOCKING; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; VALIDATION PROCESS;

ALGORITHMS; ANIMALS; BINDING SITES; COMPUTER SIMULATION; HIV PROTEASE; LIGANDS; MODELS, CHEMICAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPPING; SOFTWARE; WATER;

RUMEX;

EID: 33846000313     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21214     Document Type: Article

References (47)

1. Brooijmans N, Kuntz ID. Molecular recognition and docking algorithms. Annu Rev Biophys Biomol Struct 2003;32:335-373.
2. Halperin I, Ma B, Wolfson H, Nussinov R. Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins 2002;47:409-443.
3. Carlson HA. Protein flexibility is an important component of structure-based drug discovery. Curr Pharm Des 2002;8:1571-1578.
4. Teodoro ML, Kavraki LE. Conformational flexibility models for the receptor in structure based drug design. Curr Pharm Des 2003;9:1635-1648.
5. Teague SJ. Implications of protein flexibility for drug discovery. Nat Rev Drug Discov 2003;2:527-541.
6. Murray CW, Baxter CA, Frenkel AD. The sensitivity of the results of molecular docking to induced fit effects: application to thrombin, thermolysin and neuraminidase. J Comput Aided Mol Des 1999;13:547-562.
7. Erickson JA, Jalaie M, Robertson DH, Lewis RA, Vieth M. Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy. J Med Chem 2004;47:45-55.
8. Sherman W, Day T, Jacobson MP, Friesner RA, Farid R. Novel procedure for modeling ligand/receptor induced fit effects. J Med Chem 2006;49:534-553.
9. Apostolakis J, Pluckthun A, Caflisch A. Docking small ligands in flexible binding sites. J Comput Chem 1998;19:21-37.
10. Mangoni M, Roccatano D, Di Nola A. Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation. Proteins 1999;35:153-162.
11. Jiang F, Kim SH. Soft docking: matching of molecular surface cubes. J Mol Biol 1991;219:79-102.
12. Leach AR. Ligand docking to proteins with discrete side-chain flexibility. J Mol Biol 1994;235:345-356.
13. Abagyan R, Totrov M, Kuznetsov D. ICM-a new method for protein modeling and design-applications to docking and structure prediction from the distorted native conformation. J Comput Chem 1994;15:488-506.
14. Desmet J, Wilson IA, Joniau M, De Maeyer M, Lasters I. Computation of the binding of fully flexible peptides to proteins with flexible side-chains. FASEB J 1997;11:164-172.
15. Schaffer L, Verkhivker GM. Predicting structural effects in HIV-1 protease mutant complexes with flexible ligand docking and protein side-chain optimization. Proteins 1998;33:295-310.
16. Frimurer TM, Peters GH, Iversen LF, Andersen HS, Moller NP, Olsen OH. Ligand-induced conformational changes: improved predictions of ligand binding conformations and affinities. Biophys J 2003;84:2273-2281.
17. Sandak B, Nussinov R, Wolfson HJ. A method for biomolecular structural recognition and docking allowing conformational flexibility. J Comput Biol 1998;5:631-654.
18. Sandak B, Wolfson HJ, Nussinov R. Flexible docking allowing induced fit in proteins: insights from an open to closed conformational isomers. Proteins 1998;32:159-174.
19. Wei BQ, Weaver LH, Ferrari AM, Matthews BW, Shoichet BK. Testing a flexible-receptor docking algorithm in a model binding site. J Mol Biol 2004;337:1161-1182.
20. Knegtel RM, Kuntz ID, Oshiro CM. Molecular docking to ensembles of protein structures. J Mol Biol 1997;266:424-440.
21. Meng EC, Shoichet BK, Kuntz ID. Automated docking with grid-based energy approach to macromolecule-ligand interactions. J Comput Chem 1992;13:505-524.
22. Osterberg F, Morris GM, Sanner MF, Olson AJ, Goodsell DS. Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins 2002;46:34-40.
23. Claussen H, Buning C, Rarey M, Lengauer T. FlexE: efficient molecular docking considering protein structure variations. J Mol Biol 2001;308:377-395.
24. Ferrari AM, Wei BQ, Costantino L, Shoichet BK. Soft docking and multiple receptor conformations in virtual screening. J Med Chem 2004;47:5076-5084.
25. Broughton HB. A method for including protein flexibility in protein-ligand docking: improving tools for database mining and virtual screening. J Mol Graph Model 2000;18:247-257.
26. Carlson HA, Masukawa KM, Rubins K, Bushman FD, Jorgensen WL, Lins RD, Briggs JM, McCammon JA. Developing a dynamic pharmacophore model for HIV-1 integrase. J Med Chem 2000;43:2100-2114.
27. Meagher KL, Carlson HA. Incorporating protein flexibility in structure-based drug discovery: using HIV-1 protease as test case. J Am Chem Soc 2004;126:13276-13281.
28. Lin JH, Perryman AL, Schames JR, McCammon JA. Computational drug design accommodating receptor flexibility: the relaxed complex scheme. J Am Chem Soc 2002;124:5632-5633.
29. Lin JH, Perryman AL, Schames JR, McCammon JA. The relaxed complex method: accommodating receptor flexibility for drug design with an improved scoring scheme. Biopolymers 2003;68:47-62.
30. Zavodszky MI, Lei M, Thorpe MF, Day AR, Kuhn LA. Modeling correlated main-chain motions in proteins for flexible molecular recognition. Proteins 2004;57:243-261.
31. Cavasotto CN, Abagyan RA. Protein flexibility in ligand docking and virtual screening to protein kinases. J Mol Biol 2004;337:209-225.
32. Cavasotto CN, Kovacs JA, Abagyan RA. Representing receptor flexibility in ligand docking through relevant normal modes. J Am Chem Soc 2005;127:9632-9640.
33. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The protein data bank. Nucleic Acids Res 2000;28:235-242.
34. Ewing TJA, Makino S, Skillman AG, Kuntz ID. DOCK 4.0: search strategies for automated molecular docking of flexible molecule database. J Comput Aided Mol Des 2001;15:411-428.
35. Nelder JA, Mead R. A simplex method for function minimization. Comput J 1965;7:308-313.
36. Huang S-Y, Zou X. An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials. J Comput Chem 2006;27:1866-1875.
37. Huang S-Y, Zou X. An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function. J Comput Chem 2006;27:1876-1882.
38. Ferro DR, Hermans J. A different best rigid-body molecular fit routine. Acta Cryst A 1977;33:345-347.
39. Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE. A geometric approach to macromolecule-ligand interactions. J Mol Biol 1982;161:269-288.
40. OMEGA, OpenEye Scientific Software, Inc., Santa Fe, NM, USA, 2001. Available at http://www.eyesopen.com/.
41. Ewing TJA, Kuntz ID. Critical evaluation of search algorithms for automated molecular docking and database screening. J Comput Chem 1997;18:1175-1189.
42. Rusinko A, III, Sheridan RP, Nilakantan R, Nilakantan KS, Bauman N, Venkataraghavan R. Using CONCORD to construct a large database of three-dimensional coordinates from connection tables. J Chem Inf Comput Sci 1989;29:251-255.
43. Cole JC, Murray CW, Nissink JWM, Taylor RD, Taylor R. Comparing protein-ligand docking programs is difficult. Proteins 2005;60:325-332.
44. Charifson P, Corkery J, Murcko M, Walters WP Consensus scoring: a method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. J Med Chem 1999;42:5100-5109.
45. McGovern SL, Shoichet BK. Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes. J Med Chem 2003;46:2895-2907.
46. Muegge I, Martin YC, Hajduk PJ, Fesik SW. Evaluation of PMF scoring in docking weak ligands to the FK506 binding protein. J Med Chem 1999;42:2498-2503.
47. Barril X, Morley SD. Unveiling the full potential of flexibile receptor docking using multiple crystallographic structures. J Med Chem 2005;48:4432-4443.