Protein-ligand docking

Frontiers in Bioscience

Volumn 16, Issue 6, 2011, Pages 2289-2306

  Bottegoni, Giovanni ^a  

^a ISTITUTO ITALIANO DI TECNOLOGIA   (Italy)

Author keywords

Consensus scoring; Cross docking; Docking; Ensemble docking; Ligand docking; MRC; Protein docking; Receptor; Receptor flexibility; Review; Scoring function; Structure based drug design

Indexed keywords

CELL SURFACE RECEPTOR; LIGAND;

ALGORITHM; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER AIDED DESIGN; DRUG DESIGN; METABOLISM; MOLECULAR DYNAMICS; PROTEIN BINDING; PROTEIN CONFORMATION; REVIEW; STATISTICS;

ALGORITHMS; COMPUTER-AIDED DESIGN; DRUG DESIGN; LIGANDS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; PROTEIN CONFORMATION; RECEPTORS, CELL SURFACE; STOCHASTIC PROCESSES;

EID: 79959771257     PISSN: 27686701     EISSN: 27686698     Source Type: Journal    
DOI: 10.2741/3854     Document Type: Article

References (151)

1. E. Fischer: Einfluss der Configuration auf die Wirkung der Enzyme. Berichte der deutschen chemischen Gesellschaft, 27(3), 2985-2993 (1894)
2. J. Drews: Paul Ehrlich: Magister Mundi. Nat Rev Drug Discov, 3(9), 797-801 (2004) (Pubitemid 39242831)
3. H. Kubiny: Strategies and recent technologies in drug discovery. Pharmazie, 50(10), 647-662 (1995)
4. A. C. Anderson: The process of structure-based drug design. Chem Biol, 10(9), 787-97 (2003) (Pubitemid 37171897)
5. W. L. Jorgensen: The many roles of computation in drug discovery. Science, 303(5665), 1813-8 (2004) (Pubitemid 38374866)
6. M. Bacilieri and S. Moro: Ligand-based drug design methodologies in drug discovery process: an overview. Curr Drug Discov Technol, 3(3), 155-65 (2006) (Pubitemid 46425953)
7. A. Pozzan: Molecular descriptors and methods for ligand based virtual high throughput screening in drug discovery. Curr Pharm Des, 12(17), 2099-110 (2006) (Pubitemid 43891406)
8. J. Blaney and J. Dixon: A good ligand is hard to find: Automated docking methods. Perspectives in Drug Discovery and Design, 1(2), 301-319 (1993)
9. W. L. Jorgensen: Efficient Drug Lead Discovery and Optimization. Accounts of Chemical Research, 42(6), 724-733 (2009)
10. G. Schneider and U. Fechner: Computer-based de novo design of drug-like molecules. Nat Rev Drug Discov, 4(8), 649-63 (2005) (Pubitemid 41149759)
11. I. D. Kuntz, J. M. Blaney, S. J. Oatley, R. Langridge and T. E. Ferrin: A geometric approach to macromolecule-ligand interactions. J Mol Biol, 161(2), 269-88 (1982)
12. J. J. Gray: High-resolution protein-protein docking. Current Opinion in Structural Biology, 16(2), 183-193 (2006)
13. D. W. Ritchie: Recent progress and future directions in protein-protein docking. Curr Protein Pept Sci, 9(1), 1-15 (2008)
14. E. Karaca, A. S. J. Melquiond, S. J. de Vries, P. L. Kastritis and A. M. J. J. Bonvin: Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multi-body docking server. Molecular & Cellular Proteomics, - (2010)
15. S. Fulle and H. Gohlke: Molecular recognition of RNA: challenges for modelling interactions and plasticity. Journal of Molecular Recognition, 23(2), 220-231
16. N. Brooijmans and I. D. Kuntz: Molecular recognition and docking algorithms. Annu Rev Biophys Biomol Struct, 32, 335-73 (2003) (Pubitemid 37056233)
17. A. R. Leach, B. K. Shoichet and C. E. Peishoff: Prediction of protein-ligand interactions. Docking and scoring: successes and gaps. J Med Chem, 49(20), 5851-5 (2006) (Pubitemid 44484931)
18. K. L. Damm and H. A. Carlson: Exploring experimental sources of multiple protein conformations in structure-based drug design. J Am Chem Soc, 129(26), 8225-35 (2007) (Pubitemid 47039084)
19. H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov and P. E. Bourne: The Protein Data Bank. Nucleic Acids Res, 28(1), 235-42 (2000) (Pubitemid 30047768)
20. R. Abagyan and I. Kufareva: The flexible pocketome engine for structural chemogenomics. Methods Mol Biol, 575, 249-79 (2009)
21. M. J. Hartshorn, M. L. Verdonk, G. Chessari, S. C. Brewerton, W. T. Mooij, P. N. Mortenson and C. W. Murray: Diverse, high-quality test set for the validation of protein-ligand docking performance. J Med Chem, 50(4), 726-41 (2007) (Pubitemid 46332985)
22. P. C. Hawkins, G. L. Warren, A. G. Skillman and A. Nicholls: How to do an evaluation: pitfalls and traps. J Comput Aided Mol Des, 22(3-4), 179-90 (2008)
23. S. Y. Huang and X. Zou: Efficient molecular docking of NMR structures: application to HIV-1 protease. Protein Sci, 16(1), 43-51 (2007) (Pubitemid 46036497)
24. R. M. Knegtel, I. D. Kuntz and C. M. Oshiro: Molecular docking to ensembles of protein structures. J Mol Biol, 266(2), 424-40 (1997) (Pubitemid 27171024)
25. H. Fan, J. J. Irwin, B. M. Webb, G. Klebe, B. K. Shoichet and A. Sali: Molecular docking screens using comparative models of proteins. J Chem Inf Model, 49(11), 2512-27 (2009)
26. S. L. McGovern and B. K. Shoichet: Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes. J Med Chem, 46(14), 2895-907 (2003) (Pubitemid 36775915)
27. N. Eswar, A. Sali, B. T. John and J. T. David: Comparative Modeling of Drug Target Proteins. In: Comprehensive Medicinal Chemistry II. Elsevier, Oxford (2007)
28. P. Ferrara and E. Jacoby: Evaluation of the utility of homology models in high throughput docking. Journal of Molecular Modeling, 13(8), 897-905 (2007) (Pubitemid 47028813)
29. M. Jacobson, A. Sali and A. M. Doherty: Comparative Protein Structure Modeling and its Applications to Drug Discovery. In: Annual Reports in Medicinal Chemistry. Academic Press, (2004)
30. D. B. Kitchen, H. Decornez, J. R. Furr and J. Bajorath: Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov, 3(11), 935-49 (2004) (Pubitemid 39529931)
31. M. L. Connolly: Solvent-accessible surfaces of proteins and nucleic acids. Science, 221(4612), 709-13 (1983)
32. B. Lee and F. M. Richards: The interpretation of protein structures: estimation of static accessibility. J Mol Biol, 55(3), 379-400 (1971)
33. I. Halperin, B. Ma, H. Wolfson and R. Nussinov: Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins, 47(4), 409-43 (2002) (Pubitemid 34614722)
34. P. J. Goodford: A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J Med Chem, 28(7), 849-57 (1985) (Pubitemid 15012490)
35. A. T. Laurie and R. M. Jackson: Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening. Curr Protein Pept Sci, 7(5), 395-406 (2006) (Pubitemid 44524489)
36. G. Bottegoni, I. Kufareva, M. Totrov and R. Abagyan: A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE). J Comput Aided Mol Des, 22(5), 311-25 (2008)
37. C. N. Cavasotto and R. A. Abagyan: Protein flexibility in ligand docking and virtual screening to protein kinases. J Mol Biol, 337(1), 209-25 (2004) (Pubitemid 38270258)
38. M. L. Verdonk, G. Chessari, J. C. Cole, M. J. Hartshorn, C. W. Murray, J. W. Nissink, R. D. Taylor and R. Taylor: Modeling water molecules in protein-ligand docking using GOLD. J Med Chem, 48(20), 6504-15 (2005) (Pubitemid 41429002)
39. C. R. Corbeil and N. Moitessier: Docking ligands into flexible and solvated macromolecules. 3. Impact of input ligand conformation, protein flexibility, and water molecules on the accuracy of docking programs. J Chem Inf Model, 49(4), 997-1009 (2009)
40. E. Perola and P. S. Charifson: Conformational Analysis of Drug-Like Molecules Bound to Proteins: An Extensive Study of Ligand Reorganization upon Binding. Journal of Medicinal Chemistry, 47(10), 2499-2510 (2004) (Pubitemid 38580088)
41. W. Welch, J. Ruppert and A. N. Jain: Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites. Chemistry & Biology, 3(6), 449-462 (1996) (Pubitemid 126663345)
42. R. D. Taylor, P. J. Jewsbury and J. W. Essex: A review of protein-small molecule docking methods. J Comput Aided Mol Des, 16(3), 151-66 (2002)
43. N. Moitessier, P. Englebienne, D. Lee, J. Lawandi and C. R. Corbeil: Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go. Br J Pharmacol, 153 Suppl 1, S7-26 (2008) (Pubitemid 351340987)
44. T. J. Ewing, S. Makino, A. G. Skillman and I. D. Kuntz: DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J Comput Aided Mol Des, 15(5), 411-28 (2001) (Pubitemid 32452109)
45. M. Rarey, B. Kramer, T. Lengauer and G. Klebe: A fast flexible docking method using an incremental construction algorithm. J Mol Biol, 261(3), 470-89 (1996) (Pubitemid 26335901)
46. A. N. Jain: Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledgebased search. J Comput Aided Mol Des, 21(5), 281-306 (2007) (Pubitemid 46630055)
47. A. N. Jain: Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine. J Med Chem, 46(4), 499-511 (2003) (Pubitemid 36182752)
48. R. Abagyan and M. Totrov: High-throughput docking for lead generation. Curr Opin Chem Biol, 5(4), 375-82 (2001) (Pubitemid 32900508)
49. P. Willett: Genetic algorithms in molecular recognition and design. Trends Biotechnol, 13(12), 516-21 (1995)
50. G. M. Morris, D. S. Goodsell, R. S. Halliday, R. Huey, W. E. Hart, R. K. Belew and A. J. Olson: Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry, 19(14), 1639-1662 (1998) (Pubitemid 128590223)
51. G. Jones, P. Willett, R. C. Glen, A. R. Leach and R. Taylor: Development and validation of a genetic algorithm for flexible docking. Journal of Molecular Biology, 267(3), 727-748 (1997) (Pubitemid 27170693)
52. N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller and E. Teller: Equation of State Calculations by Fast Computing Machines. The Journal of Chemical Physics, 21(6), 1087-1092 (1953)
53. R. Abagyan, M. Totrov and D. Kuznetsov: Icm - a New Method for Protein Modeling and Design - Applications to Docking and Structure Prediction from the Distorted Native Conformation. Journal of Computational Chemistry, 15(5), 488-506 (1994)
54. R. Abagyan and M. Totrov: Biased Probability Monte- Carlo Conformational Searches and Electrostatic Calculations for Peptides and Proteins. Journal of Molecular Biology, 235(3), 983-1002 (1994) (Pubitemid 24047836)
55. R. A. Friesner, J. L. Banks, R. B. Murphy, T. A. Halgren, J. J. Klicic, D. T. Mainz, M. P. Repasky, E. H. Knoll, M. Shelley, J. K. Perry, D. E. Shaw, P. Francis and P. S. Shenkin: Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem, 47(7), 1739-49 (2004) (Pubitemid 38380917)
56. L. C. Roisman, J. Piehler, J. Y. Trosset, H. A. Scheraga and G. Schreiber: Structure of the interferon-receptor complex determined by distance constraints from doublemutant cycles and flexible docking. Proc Natl Acad Sci U S A, 98(23), 13231-6 (2001) (Pubitemid 33051345)
57. M. Liu and S. Wang: MCDOCK: a Monte Carlo simulation approach to the molecular docking problem. J Comput Aided Mol Des, 13(5), 435-51 (1999) (Pubitemid 29395560)
58. A. Cavalli, G. Bottegoni, C. Raco, M. De Vivo and M. Recanatini: A computational study of the binding of propidium to the peripheral anionic site of human acetylcholinesterase. J Med Chem, 47(16), 3991-9 (2004) (Pubitemid 38970960)
59. A. Di Nola, D. Roccatano and H. J. Berendsen: Molecular dynamics simulation of the docking of substrates to proteins. Proteins, 19(3), 174-82 (1994) (Pubitemid 24215046)
60. N. Nakajima, J. Higo, A. Kidera and H. Nakamura: Flexible docking of a ligand peptide to a receptor protein by multicanonical molecular dynamics simulation. Chemical Physics Letters, 278(4-6), 297-301 (1997) (Pubitemid 127167026)
61. F. L. Gervasio, A. Laio and M. Parrinello: Flexible docking in solution using metadynamics. J Am Chem Soc, 127(8), 2600-7 (2005) (Pubitemid 40327822)
62. M. Masetti, A. Cavalli, M. Recanatini and F. L. Gervasio: Exploring complex protein-ligand recognition mechanisms with coarse metadynamics. J Phys Chem B, 113(14), 4807-16 (2009)
63. D. E. Koshland: Application of a Theory of Enzyme Specificity to Protein Synthesis. Proc Natl Acad Sci U S A, 44(2), 98-104 (1958)
64. D. D. Boehr, R. Nussinov and P. E. Wright: The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol, 5(11), 789-96 (2009)
65. H. A. Carlson and J. A. McCammon: Accommodating protein flexibility in computational drug design. Mol Pharmacol, 57(2), 213-8 (2000) (Pubitemid 30084497)
66. F. Osterberg, G. M. Morris, M. F. Sanner, A. J. Olson and D. S. Goodsell: Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins, 46(1), 34-40 (2002) (Pubitemid 34033574)
67. M. Totrov and R. Abagyan: Flexible ligand docking to multiple receptor conformations: a practical alternative. Curr Opin Struct Biol, 18(2), 178-84 (2008)
68. F. Jiang and S. H. Kim: "Soft docking": matching of molecular surface cubes. J Mol Biol, 219(1), 79-102 (1991) (Pubitemid 121003975)
69. S. J. Teague: Implications of protein flexibility for drug discovery. Nat Rev Drug Discov, 2(7), 527-41 (2003) (Pubitemid 37361745)
70. M. Totrov and R. Abagyan: Flexible protein-ligand docking by global energy optimization in internal coordinates. Proteins, Suppl 1, 215-20 (1997) (Pubitemid 28090502)
71. A. R. Leach: Ligand docking to proteins with discrete side-chain flexibility. J Mol Biol, 235(1), 345-56 (1994) (Pubitemid 24049519)
72. E. Althaus, O. Kohlbacher, H. P. Lenhof and P. Muller: A combinatorial approach to protein docking with flexible side chains. J Comput Biol, 9(4), 597-612 (2002) (Pubitemid 35191753)
73. L. Schaffer and G. M. Verkhivker: Predicting structural effects in HIV-1 protease mutant complexes with flexible ligand docking and protein side-chain optimization. Proteins, 33(2), 295-310 (1998) (Pubitemid 28457980)
74. M. D. Daily, D. Masica, A. Sivasubramanian, S. Somarouthu and J. J. Gray: CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock. Proteins, 60(2), 181-6 (2005) (Pubitemid 40934884)
75. J. Meiler and D. Baker: ROSETTALIGAND: proteinsmall molecule docking with full side-chain flexibility. Proteins, 65(3), 538-48 (2006) (Pubitemid 44583205)
76. X. Barril and S. D. Morley: Unveiling the Full Potential of Flexible Receptor Docking Using Multiple Crystallographic Structures. J. Med. Chem., 48(13), 4432-4443 (2005) (Pubitemid 40884945)
77. R. M. A. Knegtel, I. D. Kuntz and C. M. Oshiro: Molecular docking to ensembles of protein structures. Journal of Molecular Biology, 266(2), 424-440 (1997) (Pubitemid 27171024)
78. K. D. Shoichet, I. D. Kuntz and D. L. Bodian: Molecular docking using shape descriptors. Journal of Computational Chemistry, 13(3), 380-397 (1992)
79. S. Y. Huang and X. Zou: Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking. Proteins, 66(2), 399-421 (2007) (Pubitemid 46053470)
80. T. J. A. Ewing, S. Makino, A. G. Skillman and I. D. Kuntz: DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases. Journal of Computer-Aided Molecular Design, 15(5), 411-428 (2001) (Pubitemid 32452109)
81. M. Garrett, D. Goodsell, R. Halliday, R. Huey, W. Hart, R. Belew and A. J. Olson: Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry, 19(14), 1639-1662 (1998) (Pubitemid 128590223)
82. T. Polgar and G. M. Keseru: Ensemble docking into flexible active sites. Critical evaluation of FlexE against JNK-3 and beta-secretase. J Chem Inf Model, 46(4), 1795-805 (2006) (Pubitemid 44185704)
83. H. Claussen, C. Buning, M. Rarey and T. Lengauer: FlexE: efficient molecular docking considering protein structure variations. J Mol Biol, 308(2), 377-95 (2001) (Pubitemid 33043576)
84. S. Rao, P. C. Sanschagrin, J. R. Greenwood, M. P. Repasky, W. Sherman and R. Farid: Improving database enrichment through ensemble docking. J Comput Aided Mol Des, 22(9), 621-7 (2008)
85. M. Rueda, G. Bottegoni and R. Abagyan: Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes. J Chem Inf Model, 49(3), 716-25 (2009)
86. G. Bottegoni, I. Kufareva, M. Totrov and R. Abagyan: Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking. J Med Chem, 52(2), 397-406 (2009)
87. C. R. Corbeil, P. Englebienne and N. Moitessier: Docking ligands into flexible and solvated macromolecules. 1. Development and validation of FITTED 1.0. J Chem Inf Model, 47(2), 435-49 (2007) (Pubitemid 46615946)
88. Y. Zhao and M. F. Sanner: FLIPDock: docking flexible ligands into flexible receptors. Proteins, 68(3), 726-37 (2007) (Pubitemid 47068311)
89. W. Sherman, T. Day, M. P. Jacobson, R. A. Friesner and R. Farid: Novel procedure for modeling ligand/receptor induced fit effects. J Med Chem, 49(2), 534-53 (2006) (Pubitemid 43157487)
90. J. H. Lin, A. L. Perryman, J. R. Schames and J. A. McCammon: Computational drug design accommodating receptor flexibility: the relaxed complex scheme. J Am Chem Soc, 124(20), 5632-3 (2002) (Pubitemid 34533490)
91. R. E. Amaro, R. Baron and J. A. McCammon: An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J Comput Aided Mol Des, 22(9), 693-705 (2008)
92. G. M. Morris, R. Huey, W. Lindstrom, M. F. Sanner, R. K. Belew, D. S. Goodsell and A. J. Olson: AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem, 30(16), 2785-91 (2009)
93. P. A. Kollman, I. Massova, C. Reyes, B. Kuhn, S. H. Huo, L. Chong, M. Lee, T. Lee, Y. Duan, W. Wang, O. Donini, P. Cieplak, J. Srinivasan, D. A. Case and T. E. Cheatham: Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Accounts of Chemical Research, 33(12), 889-897 (2000) (Pubitemid 32056774)
94. D. C. Thompson, C. Humblet and D. Joseph-McCarthy: Investigation of MM-PBSA rescoring of docking poses. Journal of Chemical Information and Modeling, 48(5), 1081-1091 (2008)
95. M. S. Lee and M. A. Olson: Calculation of absolute protein-ligand binding affinity using path and endpoint approaches. Biophysical Journal, 90(3), 864-877 (2006)
96. J. M. J. Swanson, R. Henchman and J. A. McCammon: Revisiting free energy calculations: One step closer to rigorous scoring functions and one step beyond MM/PBSA. Abstracts of Papers of the American Chemical Society, 227, U903-U904 (2004)
97. J. R. Schames, R. H. Henchman, J. S. Siegel, C. A. Sotriffer, H. Ni and J. A. McCammon: Discovery of a novel binding trench in HIV integrase. J Med Chem, 47(8), 1879-81 (2004) (Pubitemid 38453905)
98. A. Babakhani, T. T. Talley, P. Taylor and J. A. McCammon: A virtual screening study of the acetylcholine binding protein using a relaxed-complex approach. Comput Biol Chem, 33(2), 160-70 (2009)
99. J. D. Durrant, C. A. F. de Oliveira and J. A. McCammon: Including receptor flexibility and induced fit effects into the design of MMP-2 inhibitors. Journal of Molecular Recognition, 23(2), 173-182 (2010)
100. S. A. Hassan, L. Gracia, G. Vasudevan and P. J. Steinbach: Computer simulation of protein-ligand interactions: challenges and applications. Methods Mol Biol, 305, 451-92 (2005)
101. H. Gohlke and G. Klebe: Approaches to the description and prediction of the binding affinity of smallmolecule ligands to macromolecular receptors. Angew Chem Int Ed Engl, 41(15), 2644-76 (2002)
102. M. K. Gilson and H. X. Zhou: Calculation of proteinligand binding affinities. Annu Rev Biophys Biomol Struct, 36, 21-42 (2007)
103. P. Kollman: Free energy calculations: Applications to chemical and biochemical phenomena. Chemical Reviews, 93(7), 2395-2417 (1993)
104. J. G. Kirkwood: Statistical Mechanics of Fluid Mixtures. The Journal of Chemical Physics, 3(5), 300-313 (1935)
105. W. L. Jorgensen: Efficient drug lead discovery and optimization. Acc Chem Res, 42(6), 724-33 (2009)
106. A. Laio and M. Parrinello: Escaping free-energy minima. Proc Natl Acad Sci U S A, 99(20), 12562-6 (2002)
107. J. Aqvist, C. Medina and J. E. Samuelsson: New Method for Predicting Binding-Affinity in Computer-Aided Drug Design. Protein Engineering, 7(3), 385-391 (1994) (Pubitemid 24063137)
108. T. Simonson, G. Archontis and M. Karplus: Free energy simulations come of age: Protein-ligand recognition. Accounts of Chemical Research, 35(6), 430-437 (2002)
109. P. Ferrara, H. Gohlke, D. J. Price, G. Klebe and C. L. Brooks, 3rd: Assessing scoring functions for protein-ligand interactions. J Med Chem, 47(12), 3032-47 (2004) (Pubitemid 38702700)
110. P. Cieplak, J. Caldwell and P. Kollman: Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: Aqueous solution free energies of methanol and N-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases. Journal of Computational Chemistry, 22(10), 1048-1057 (2001) (Pubitemid 32614376)
111. B. Kramer, M. Rarey and T. Lengauer: Evaluation of the FLEXX incremental construction algorithm for proteinligand docking. Proteins, 37(2), 228-41 (1999) (Pubitemid 29503004)
112. N. Gresh: Development, validation, and applications of anisotropic polarizable molecular mechanics to study ligand and drug-receptor interactions. Curr Pharm Des, 12(17), 2121-58 (2006) (Pubitemid 43891408)
113. M. Totrov and R. Abagyan: Derivation of sensitive discrimination potential for virtual screening. In: RECOMB '99. Proceedings of the Third Annual International Conference on Computational Molecular Biology. ACM Press - New York, Lyon (France) (1999)
114. M. D. Eldridge, C. W. Murray, T. R. Auton, G. V. Paolini and R. P. Mee: Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J Comput Aided Mol Des, 11(5), 425-45 (1997) (Pubitemid 127505895)
115. P. Cozzini, M. Fornabaio, A. Marabotti, D. J. Abraham, G. E. Kellogg and A. Mozzarelli: Simple, intuitive calculations of free energy of binding for protein-ligand complexes. 1. Models without explicit constrained water. J Med Chem, 45(12), 2469-83 (2002) (Pubitemid 34595216)
116. R. D. Head, M. L. Smythe, T. I. Oprea, C. L. Waller, S. M. Green and G. R. Marshall: VALIDATE: A New Method for the Receptor-Based Prediction of Binding Affinities of Novel Ligands. Journal of the American Chemical Society, 118(16), 3959-3969 (1996) (Pubitemid 26168541)
117. H. J. Bohm: LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads. J Comput Aided Mol Des, 6(6), 593-606 (1992)
118. G. Klebe and T. Mietzner: A fast and efficient method to generate biologically relevant conformations. J Comput Aided Mol Des, 8(5), 583-606 (1994)
119. I. Muegge and Y. C. Martin: A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J Med Chem, 42(5), 791-804 (1999) (Pubitemid 29136170)
120. H. Gohlke and G. Klebe: Statistical potentials and scoring functions applied to protein-ligand binding. Curr Opin Struct Biol, 11(2), 231-5 (2001) (Pubitemid 32289427)
121. A. V. Ishchenko and E. I. Shakhnovich: SMall Molecule Growth 2001 (SMoG2001): an improved knowledge-based scoring function for protein-ligand interactions. J Med Chem, 45(13), 2770-80 (2002) (Pubitemid 34627647)
122. C. Y. Yang, R. Wang and S. Wang: M-score: a knowledge-based potential scoring function accounting for protein atom mobility. J Med Chem, 49(20), 5903-11 (2006) (Pubitemid 44484937)
123. P. S. Charifson, J. J. Corkery, M. A. Murcko and W. P. Walters: Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. J Med Chem, 42(25), 5100-9 (1999) (Pubitemid 30020261)
124. N. Paul and D. Rognan: ConsDock: A new program for the consensus analysis of protein-ligand interactions. Proteins, 47(4), 521-33 (2002) (Pubitemid 34614732)
125. R. Wang and S. Wang: How does consensus scoring work for virtual library screening? An idealized computer experiment. J Chem Inf Comput Sci, 41(5), 1422-6 (2001)
126. G. Bottegoni, W. Rocchia, M. Recanatini and A. Cavalli: AClAP, Autonomous hierarchical agglomerative Cluster Analysis based protocol to partition conformational datasets. Bioinformatics, 22(14), e58-65 (2006) (Pubitemid 44288273)
127. G. Bottegoni, A. Cavalli and M. Recanatini: A comparative study on the application of hierarchicalagglomerative clustering approaches to organize outputs of reiterated docking runs. J Chem Inf Model, 46(2), 852-62 (2006)
128. C. Bissantz, G. Folkers and D. Rognan: Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. J Med Chem, 43(25), 4759-67 (2000) (Pubitemid 32002687)
129. B. D. Bursulaya, M. Totrov, R. Abagyan and C. L. Brooks, 3rd: Comparative study of several algorithms for flexible ligand docking. J Comput Aided Mol Des, 17(11), 755-63 (2003) (Pubitemid 38418287)
130. T. Cheng, X. Li, Y. Li, Z. Liu and R. Wang: Comparative assessment of scoring functions on a diverse test set. J Chem Inf Model, 49(4), 1079-93 (2009)
131. J. B. Cross, D. C. Thompson, B. K. Rai, J. C. Baber, K. Y. Fan, Y. Hu and C. Humblet: Comparison of several molecular docking programs: pose prediction and virtual screening accuracy. J Chem Inf Model, 49(6), 1455-74 (2009)
132. M. Kontoyianni, L. M. McClellan and G. S. Sokol: Evaluation of docking performance: comparative data on docking algorithms. J Med Chem, 47(3), 558-65 (2004) (Pubitemid 38129714)
133. J. C. Cole, C. W. Murray, J. W. Nissink, R. D. Taylor and R. Taylor: Comparing protein-ligand docking programs is difficult. Proteins, 60(3), 325-32 (2005) (Pubitemid 41061629)
134. G. L. Warren, C. W. Andrews, A. M. Capelli, B. Clarke, J. LaLonde, M. H. Lambert, M. Lindvall, N. Nevins, S. F. Semus, S. Senger, G. Tedesco, I. D. Wall, J. M. Woolven, C. E. Peishoff and M. S. Head: A critical assessment of docking programs and scoring functions. J Med Chem, 49(20), 5912-31 (2006) (Pubitemid 44484938)
135. M. Congreve, G. Chessari, D. Tisi and A. J. Woodhead: Recent developments in fragment-based drug discovery. J Med Chem, 51(13), 3661-80 (2008) (Pubitemid 351956496)
136. R. Morphy and Z. Rankovic: Fragments, network biology and designing multiple ligands. Drug Discov Today, 12(3-4), 156-60 (2007) (Pubitemid 46176667)
137. J. D. Durrant, R. E. Amaro, L. Xie, M. D. Urbaniak, M. A. Ferguson, A. Haapalainen, Z. Chen, A. M. Di Guilmi, F. Wunder, P. E. Bourne and J. A. McCammon: A multidimensional strategy to detect polypharmacological targets in the absence of structural and sequence homology. PLoS Comput Biol, 6(1), e1000648 (2010)
138. Y. Chen and B. K. Shoichet: Molecular docking and ligand specificity in fragment-based inhibitor discovery. Nat Chem Biol, 5(5), 358-64 (2009)
139. G. Marcou and D. Rognan: Optimizing fragment and scaffold docking by use of molecular interaction fingerprints. J Chem Inf Model, 47(1), 195-207 (2007) (Pubitemid 46237537)
140. R. E. Hubbard, I. Chen and B. Davis: Informatics and modeling challenges in fragment-based drug discovery. Curr Opin Drug Discov Devel, 10(3), 289-97 (2007) (Pubitemid 46800223)
141. R. Morphy, C. Kay and Z. Rankovic: From magic bullets to designed multiple ligands. Drug Discov Today, 9(15), 641-51 (2004) (Pubitemid 38981718)
142. A. V. Grigoryan, I. Kufareva, M. Totrov and R. A. Abagyan: Spatial chemical distance based on atomic property fields. J Comput Aided Mol Des (2010)
143. M. Totrov: Atomic property fields: generalized 3D pharmacophoric potential for automated ligand superposition, pharmacophore elucidation and 3D QSAR. Chem Biol Drug Des, 71(1), 15-27 (2008)
144. J. Gora-Tybor and T. Robak: Targeted drugs in chronic myeloid leukemia. Curr Med Chem, 15(29), 3036-51 (2008)
145. F. J. Giles, J. E. Cortes and H. M. Kantarjian: Targeting the kinase activity of the BCR-ABL fusion protein in patients with chronic myeloid leukemia. Curr Mol Med, 5(7), 615-23 (2005) (Pubitemid 41824225)
146. S. Schenone, F. Manetti and M. Botta: Last findings on dual inhibitors of abl and SRC tyrosine-kinases. Mini Rev Med Chem, 7(2), 191-201 (2007) (Pubitemid 46592182)
147. F. Manetti, G. A. Locatelli, G. Maga, S. Schenone, M. Modugno, S. Forli, F. Corelli and M. Botta: A combination of docking/dynamics simulations and pharmacophoric modeling to discover new dual c-Src/Abl kinase inhibitors. J Med Chem, 49(11), 3278-86 (2006) (Pubitemid 43830525)
148. D. Wei, X. Jiang, L. Zhou, J. Chen, Z. Chen, C. He, K. Yang, Y. Liu, J. Pei and L. Lai: Discovery of Multitarget Inhibitors by Combining Molecular Docking with Common Pharmacophore Matching. Journal of Medicinal Chemistry, 51(24), 7882-7888 (2008)
149. E. Jenwitheesuk, J. A. Horst, K. L. Rivas, W. C. Van Voorhis and R. Samudrala: Novel paradigms for drug discovery: computational multitarget screening. Trends in Pharmacological Sciences, 29(2), 62-71 (2008)
150. G. M. Verkhivker, D. Bouzida, D. K. Gehlhaar, P. A. Rejto, S. Arthurs, A. B. Colson, S. T. Freer, V. Larson, B. A. Luty, T. Marrone and P. W. Rose: Deciphering common failures in molecular docking of ligand-protein complexes. J Comput Aided Mol Des, 14(8), 731-51 (2000)
151. B. K. Shoichet, S. L. McGovern, B. Wei and J. J. Irwin: Lead discovery using molecular docking. Curr Opin Chem Biol, 6(4), 439-46 (2002) (Pubitemid 34808727)