Virtual screening

Comprehensive Medicinal Chemistry II

Volumn 4, Issue , 2006, Pages 459-494

  Good, A ^a  

^a BRISTOL MYERS SQUIBB   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77958027763     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (358)

1. Virtml Screening for Bioactive Molecules; Böhm, H.-J., Schneider, G., Kubinyi, H., Mannhold, R., Timmerman, H., Eds.; Wiley-VCH: New York, 2000.
2. Virtual Screening: An Alternative or Complement to High Throughput Screening; Klebe, G., Ed.; Springer: New York, 2000.
3. Good, A. G.; Krystek, S.; Mason, J. S. Drug Disc. Today 2000, 5, 61-65.
4. Seifert, M. H. J.; Wolf, K.; Vitt, D. Biosilico 2003, 1, 143-149.
5. Oprea, T I.; Matter, H. Curr. Opin. Chem. Biol. 2004, 8, 349-358.
6. Stahura, E; Bajorath, Comb. Chem. & H.T.S. 2004, 7, 259-269.
7. Lengauar, T; Lemmen, G.; Rarey, M.; Zimmerman, M. Drug Disc. Today 2004, 9, 27-34.
8. Olah, M. M.; Bologa, G. G.; Oprea, T I. Curr. Drug Disc. Tech. 2004, 1, 211-220.
9. Virtual Screening in Drug Discovery; Alvarez, J., Schoichet, B., Eds.; GRG Press: Boca Raton, FL, 2005.
10. Willett, P. J. Chemometrics 1987, 1, 139-146.
11. Dalby, A.; Nourse, J. G.; Hounshell, W D.; Gushurst, A. Κ. I.; Grier, D. L.; Leland, B. A.; Läufer, J. J. Chem. Inf. Comput. Sei. 1992,32, 244-255.
12. Gramer, R. D.; Redl, G.; Berkoff, G. E. J. Med. Chem. 1974, 17, 533-535.
13. Tarjan, R. E. Graph Algorithms in Chemical Computation. In Algorithms for Chemical Computations; American Chemical Society: Washington, DC, 1977, pp 1-20.
14. Barnard, J. M. J. Chem. Inf. Comput. Sei. 1993, 33, 532-538.
15. Milne, G. W. A. J. Chem. Inf. Comput. Sei. 1997, 374, 639-644.
16. See mol2athttp://www.tripos.com/(accessed April 2006).
17. Weininger, D. J. Chem. Inf. Comput. Sei. 1988, 28, 31-37.
18. SMILES and SMARTS, developed and distributed by Daylight Chemical Information Systems: http://www.dayhght.com/dayhtml/(accessed April 2006).
19. Ash, S.; Cline, M. A.; Homer, W. R.; Hurst, T; Smith, G. B. J. Chem. Inf. Comput. Sei. 1997, 371, 71-79.
20. Lynch, M. E; Downs, G. M. Chemical Patent Database Systems. In Chemical Structure Systems: Computational Techniques for Representation, Searching, and Processing of Structural Information; Ash, J. E., Warr, W A., Willett, P., Eds.; Ellis Horwood: Chichester, UK, 1991, pp 126-153.
21. Corey, E. J.; Feiner, N. E. J. Org. Chem. 1980, 45, 757-764.
22. Corey, E. J.; Feiner, N. E. J. Org. Chem. 1980, 45, 765-780.
23. Hoflack, J.; De Glercq, P. J. Tetrahedron 1988, 4421, 6667-6676.
24. SCA, QCPE Program QCMP079. Bloomington, IN, USA, Quantum Chemistry Program Exchange. Indiana University, 1989. http://qcpe.chem.indiana.edu/(accessed April 2006).
25. Rarey, M.; Kramer, B.; Lengauer, T; Klebe, G. J. Mol. Biol. 1996, 261, 470-489.
26. FlexX, developed and distributed by BioSolvelT gmbh: http://www.biosolveit.de (accessed April 2006).
27. Leach, A. R.; Prout, K.; Dolata, D. P. J. Comput.-Aided Mol. Des. 1990, 4, 271-282.
28. Dolata, D. P.; Leach, A. R.; Prout, K. J. Comput.-Aided Mol. Des. 1987, 1, 73-85.
29. Leach, A. R.; Dolata, D. P.; Prout, K. J. Chem. Inf. Comput. Sei. 1990, 30, 316-324.
30. Leach, A. R. J. Chem. Inf. Comput. Sei. 1994, 34, 661-670.
31. Havel, T. E; Kuntz, I. D.; Grippen, G. M. J. Theor. Biol. 1983, 1043, 359-381.
32. Crippen, G. M.; Havel, T. E. Distance Geometry and Molecular Conformations. In Chemometrics; Bawden, D., Ed.; Research Studies Series 15; Research: New York, 1988, pp 101-122.
33. Grippen, G. M.; Havel, I. E. J. Chem. Inf. Comput. Sei. 1990, 30, 222-227.
34. DGEOM, QCPE Program No. 590. Bloomington, IN, USA, Quantum Chemistry Program Exchange, Indiana University, 1995. http://qcpe.chem.Indiana.edu/(accessed April 2006).
35. CONCORD, STEREOPLEX, PROTOPLEX, and CONFORTare distributed by Tripos Inc. http://www.tripos.comsol (accessed April 2006).
36. Pearlman, R. S. Chem. Des. Autom. News 1987, 2, 5-6.
37. Pearlman, R. S.; Stewart, E. L.; Smith, K. M.; Balducci, R. Book of Abstracts, 211th American Chemical Society National Meeting, New Orleans, LA, March 24-28, 1996; CINF-065.
38. Pearlman, R. S.; Khashan, R.; Wong, D.; Balducci, R. Book of Abstracts, 224th American Chemical Society National Meeting, Boston, MA, Aug 18-22, 2002; COMP-232.
39. Sadowski, J.; Gasteiger, J. J. Chem. Rev. 1993, 7, 2567-2581.
40. Sadowski, J. Three Dimensional Structure Generation: Automation. In Encyclopedia of Computational Chemistry; Schleyer, R R., Allinger, N. L., Clark, T., Gasteiger, J., Kollman, R A., Shaefer, H. E, III., Scheiner, P. R., Eds.; John Wiley: Chichester, UK, 1998, pp 2976-2988.
41. CORINA, developed and distributed by the University of Erlangen, http://www2.chemie.uni-erlangen.de/software/(accessed April 2006).
42. Dale, J. Acta Chem. Scand. 1973, 27, 1115-1129.
43. Klebe, G.; Mietzner, T; Weber, E. J. Comput.-Aided Mol. Des. 1999, 13, 35-49.
44. Cambridge Structural Database. http://www.ccdc.cam.ac.uk/products/csd/(accessed April 2006).
45. Confirm and Catalyst, developed and distributed by Accelrys Inc. http://www.accelrys.com/catalyst/(accessed April 2006).
46. DGII, distributed by Accelrys Inc. http://www.accelrys.com (accessed April 2006). See also http://www.scripps.edu/rc/softwaredocs/msi/insight2K/CONVERTER/02_Theory.html.#661284 (accessed April 2006).
47. Havel, T. F. Biopolymers 1990, 2912, 1565-1585.
48. Omega and Qu A. C. P. A. C, developed and distributed by Openeye Scientific Software. http://www.eyesopen.com/(accessed April 2006).
49. Stahl, M. T; Nicholls, A.; Anthony, R. A; Grant, A. J. Book of Abstracts, 217th American Chemical Society National Meeting, Anaheim, CA, March 21-25, 1999; COMP-026.
50. Stahl, M.; Skillman, G. Abstracts of Papers, 229th American Chemical Society National Meeting, San Diego, CA, March 13-17, 2005; COMP-141.
51. Spellmeyer, D. C.; Wong, A. K.; Bower, M. J.; Blaney, J. M. J. Mol. Graph. Model. 1997, 15, 18-36.
52. Halgren, T A. J. Comp. Chem. 1999, 20, 730-748.
53. LIGPREP, developed and distributed by Schrodinger Inc. http://www.schrodinger.com/(accessed April 2006).
54. JAGUAR quantum mechanical software, developed and distributed by Schrodinger Inc. http://www.schrodinger.com (accessed April 2006).
55. Chang, G.; Guida, W C.; Still, W C. J. Am. Chem. Soc. 1989, 111, 4379-4384.
56. Saunders, M.; Houk, K. N.; Wu, Y D.; Still, C. W; Lipton, M.; Chang, G.; Guida, W C. J. Am. Chem. Soc. 1990, 112, 1419-1429.
57. MACROMODEL, developed and distributed by Schrodinger Inc. http://www.schrodinger.com/(accessed April 2006).
58. Smellie, A.; Kahn, S. D.; Teig, S. L. J. Chem. Inf. Comput. Sei. 1995, 35, 285-294.
59. Smellie, A.; Kahn, S. D.; Teig, S. L. J. Chem. Inf. Comput. Sei. 1995, 35, 295-304.
60. Smellie, A.; Teig, S. L.; Towbin, P J. Comput. Chem. 1995, 16, 171-187.
61. Murrall, N. W.; Davies, E. K. J. Chem. Inf. Comput. Sei., 1990, 30, 312-316.
62. Ewing, T J. A.; Kuntz, I. D. J. Comput. Chem. 1997, 189, 1175-1189.
63. Balducci, R.; Pearlman, R. S. Book of Abstracts, 217th American Chemical Society National Meeting, Anaheim, CA, March 21-25 1999; COMP-011.
64. RUBICON, developed and distributed by Daylight Chemical Information Systems. http://www.daylight.com/(accessed April 2006).
65. Mayo, S. L.; Olafson, B. D.; Goddard, W A., III. J. Phys. Chem. 1990, 9426, 8897-8909.
66. Sykes, M.; Pickup, B; Grant, J. A. The Sheffield Solvation Model, In preparation.
67. Hurst, T. J. Chem. Inf. Comput. Sei. 1994, 34, 190-196.
68. UNITY, developed and distributed by Tripos Inc. http://www.tripos.com/(accessed April 2006).
69. Moock, T. E.; Henry, D. R.; Ozkabak, A. G.; Alamgir, M. J. Chem. Inf. Comput. Sei. 1994, 34, 184-189.
70. ISIS-3D, developed and distributed by MDL Information Systems Inc. http://www.mdl.com/(accessed April 2006).
71. Lemmen, C.; Lengauer, T; Klebe, G. J. Med. Chem. 1998, 4123, 4502-4520.
72. Lemmen, C.; Zimmermann, M.; Lengauar, T. Perspect. Drug Disc. Des. 2000, 20, 43-62.
73. FlexS, developed and distributed by BioSolveIT gmbh: http://www.biosolveit.de/(accessed April 2006).
74. Sadowski, J.; Schwab, C. H.; Gasteiger, J. http://www2.chemie.uni-erlangen.de/(accessed July 2006).
75. Sadowski, J.; Gasteiger, J.; Klebe, G. J. Chem. Inf. Comput. Sei. 1994, 34, 1000-1008.
76. Green, D. V S. In Des. Bioact. Mol.; Martin, Y C.; Willet, P., Eds.; American Chemical Society: Washington, DC, 1998, pp 47-71.
77. Van Geerestein, V. J.; Verwer, P. Book of Abstracts, 211th American Chemical Society National Meeting, New Orleans, LA, March 24-28, 1996, CINF038.
78. Sadowski, J.; Schwab, C. H.; Gasteiger, J. 3D Structure Generation and Conformational Searching. In Computational Medicinal Chemistry for Drug Discovery; Bultinck, P, de Winter, H., Langenaeker, W, Tollenaere, J. P., Eds.; Marcel Dekker: New York, 2004, pp 151-212.
79. Daylight Chemical Information System Inc. http://www.daylight.com/meetings/(accessed April 2006).
80. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T N.; Weissig, H.; Shindyalov, I. N.; Bourne, P E. Nud. Adds Res. 2000, 28, 235-242.
81. Ricketts, E. M.; Bradshaw, J.; Hann, M. M.; Hayes, F; Tanna, N.; Ricketts, D. M. J. Chem. Inf. Comput. Sei. 1993, 33, 905-925.
82. Boström, J. J. Comput.-Aided Mol. Des. 2001, 1512, 1137-1152.
83. Good, A. C.; Cheney, D. L. J. Mol. Graph. Model. 2003, 221, 23-30.
84. Perola, E.; Charifson, P S. J. Med. Chem. 2004, 47, 2499-2510.
85. Ray, L. C.; Kirsch, R. A. Science 1957, 126, 814-819.
86. Downs, G. M.; Willett, P. Similarity Searching in Databases of Chemical Structures. In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; VCH: New York, 1996; Vol. 7, pp 1-66.
87. Ullmann, J. R. J. Assoc. Comput. Mach. 1976, 23, 31-42.
88. Downs, G. M.; Lynch, M. E.; Willett, P.; Manson, G. A.; Wilson, G. A. Tetrahedron Comput. 1988, 1, 207-217.
89. Lynch, M. E. Screening Large Chemical Files. In Chemical Information Systems; Ash, J. E., Hyde, E., Eds.; John Wiley: Chichester, UK, 1974, pp 177-194.
90. Bartmann, A.; Maier, H.; Roth, B.; Walkowiak, D. J. Chem. Inf. Comput. Sci. 1990, 33, 539-541.
91. Graf, W.; Kaindl, H. K.; Kneiss, H.; Schmidt, B.; Warszawski, R. J. Chem. Inf. Comput. Sci. 1982, 22, 177-181.
92. Isis and Crossfire, developed and distributed by MDL Information Systems. http://www.mdl.com/(accessed April 2006).
93. Merlin, developed and distributed by Daylight Chemical Information Systems Inc. http://www.daylight.com/products/(accessed April 2006).
94. UNITY, developed and distributed by Tripos Inc. http://www.tripos.com/(accessed April 2006).
95. Good, A. C.; Mason, J. S. In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; VCH: New York, 1996; Vol. 7, pp 67-127.
96. Milne, G. W A.; Nicklaus, M. C.; Wang, S. SAR QSAR Environ. Res. 1998, 9, 23-38.
97. Warr, W A.; Willett, P. In Des. Bioact. Mol.; Martin, Y C.; Willet, P., Eds.; American Chemical Society: Washington, DC, 1998, pp 73-95.
98. Pharmacophore Perception, Development, and Use in Drug Design; Guner, O. F, Ed.; International University Line: La Jolla, CA, 2000.
99. Good, A. C. Mason, J. S.; Pickett, S. D. Pharmacophore Pattern Application in Virtual Screening, Library Design and QSAR. In Virtual Screening for Bioactive Molecules; Bohm, H.-J., Schneider, G., Ed.; John Wiley: New York, 2000; Vol. 10, pp 131-154.
100. van Drie, J. H. Curr. Pharm. Des. 2003, 920, 1649-1664.
101. Marshall, G. R. Binding Site Modeling of Unknown Receptors. In 3D QSAR in Drug Design; Kubinyi, H., Ed.; ESCOM: Leiden, The Netherlands, 1993, pp 80-116.
102. Van Drie, J. H.; Weiniger, D.; Martin, Y C. J. Comput.-Aided Mol. Des. 1989, 3, 225-251.
103. Phase, developed and distributed by Schrodinger Inc. http://www.schrodinger.com/(accessed April 2006).
104. MOE, Molecular Operating Environment. Distributor: Chemical Computing Group. http://www.chemcomp.com/(accessed April 2006).
105. Wang, S.; Milne, G. W A.; Yan, X.; Posey, I. J.; Nicklaus, M. C.; Graham, L.; Rice, W G. J. Med. Chem. 1996, 39, 2047-2054.
106. Hong, H.; Neamati, N.; Wang, S.; Nicklaus, M. C.; Mazumder, A.; Zhao, H.; Burke, T. R., Jr.; Pommier, Y; Milne, G. W A. J. Med. Chem. 1997, 40, 930-936.
107. Marriott, D. P.; Dougall, I. G.; Meghani, P; Liu, Y-J.; Flower, D. R. J. Med. Chem. 1999, 42, 3210-3216.
108. Singh, J.; van Vlijmen, H.; Liao, Y; Lee, W-C.; Cornebise, M.; Harris, M.; Shu, I.-H.; Gill, A.; Cuervo, J. H.; Abraham, W M.; Adams, S. P. J. Med. Chem. 2002, 45, 2988-2993.
109. Clark, D. E.; Higgs, C.; Wren, S. P; Dyke, H. J.; Wong, M.; Norman, D.; Lockey, P. M.; Roach, A. G. J. Med. Chem. 2004, 47, 3962-3971.
110. Pirard, B.; Brendel, J.; Peukert, S. J. Chem. Inf. Model. 2005, 452, 477-485.
111. Ekins, S.; Johnston, J. S.; Bahadduri, P; D'Souza, V. M.; Ray, A.; Chang, C.; Swaan, P. W. Pharm. Res. 2005, 224, 512-517.
112. Steindl, T. M.; Crump, C. E.; Hayden, F. G.; Langer, T. J. Med. Chem. 2005, 48, 6250-6260.
113. Sheridan, R. P.; Miller, M. D. J. Chemut. Inf. Comput. Sei. 1998, 385, 915-924.
114. Chen, L. Substructure and Maximum Common Substructure Searching. In Computational Medicinal Chemistry for Drug Discovery; Bultinck, P, de Winter, H., Langenaeker, W., Tollenaere, J. P., Eds.; Marcel Dekker: New York, 2004, pp 483-511.
115. Martin, Y C.; Bures, M. G.; Danaher, E. A.; DeLazzer, J.; Lico, I.; Pavlik, P. A. J. Comput.-Aided Mol. Des. 1993, 7, 83-102.
116. DISCO, distributed by Tripos Inc. http://www.tripos.com/(accessed April 2006).
117. Brint, A. T; Willett, P. J. J. Chem. Inf. Comput. Sci. 1987, 27, 152-158.
118. Jones, G.; Willett, P.; Glen, R. C. J. Comput.-Aided Mol. Des. 1995, 96, 532-549.
119. Lemmen, C.; Lengauer, T; Klebe, G. J. Med. Chem. 1998, 4123, 4502-4520.
120. Miller, M. D.; Sheridan, R. P; Kearsley, S. K. J. Med. Chem. 1999, 429, 1505-1514.
121. HypoGen, developed and distributed by Accelrys Inc. http://www.accelrys.com/(accessed April 2006).
122. Gasp, distributer by Tripos Inc. http://www.tripos.com/(accessed April 2006).
123. Durant, J. L.; Leland, B. A.; Henry, D. R.; Nourse, J. G. J. Chem. Inf. Comput. Sci. 2002, 42, 1273-1280.
124. BCI fingerprints, part of the BCI toolkit, developed and distributed by Barnard Chemical Information Ltd. http://www.bci.gb.com/(accessed April 2006).
125. McGregor, M. J.; Muskal, S. M. J. Chem. Inf. Comput. Sci. 1999, 39, 569-574.
126. Mason, J. S.; Morize, I.; Menard, P R.; Cheney, D. L.; Hulme, C.; Labaudiniere, R. F. J. Med. Chem. 1999, 4217, 3251-3264.
127. Carhart, R. E.; Smith, D. H.; Venkataraghavan, R. J. Chem. Inf. Comput. Sci. 1985, 25, 64-73.
128. Daylight Chemical Information System Inc. http://www.daylight.com/(accessed April 2006).
129. ECFP and FCFP fingerprints, part of Pipeline Pilot, developed and distributed by Scitegic. http://www.scitegic.com/(accessed April 2006).
130. Sheridan, R. P.; Miller, M. D.; Underwood, D. J.; Kearsley, S. K. J. Chem. Inf. Comput. Sci. 1996, 36, 128-136.
131. Pearlman, R. S.; Smith, K. M. J. Chem. Inf. Comput. Sci. 1999, 39, 28-35.
132. Willett, P; Winterman, V; Bawden, D. J. Chem. Inf. Comput. Sci. 1986, 26, 36-41.
133. Christie, A. D.; Leland, B. A.; Nourse, I. G. J. Chem. Inf. Comput. Sci. 1993, 33, 545-547.
134. Brown, R. D.; Martin, Y C. J. Chem. Inf. Comput. Sci. 1996, 36, 572-584.
135. Barnard, J. M.; Downs, G. M. J. Chem. Inf. Comput. Sci. 1997, 37, 141-142.
136. 2003 User Group Meeting http://www.scitegic.com/newsevent/(accessed April 2006).
137. Willett, P. J. Chem. Inf. Comput. Sci. 1979, 19, 159-162.
138. Nilakantan, R.; Bauman, N.; Dixon, S. J.; Venkataraghavan, R. J. Chem. Inf. Comput. Sci. 1987, 27, 82-85.
139. Kearsley, S. K.; Sallamack, S.; Fluder, E. M.; Andose, J. D.; Mosley, R. T.; Sheridan, R. P. J. Chem. Inf. Comput. Sci. 1996, 361, 118-127.
140. Schuffenhauer, A.; Floersheim, P.; Acklin, P; Jacoby, E. J. Chem. Inf. Comput. Sci. 2003, 432, 391-405.
141. Klein, K.; Lehmann, C. W; Schmidt, H.-W; Maier, W. F. Angew. Chem. 1998, 110, 3369-3372.
142. Schneider, G.; Neidhart, W; Giller, T; Schmid, G. Angew. Chem. Int. Ed. Engl. 1999, 38, 2894-2896.
143. Bemis, G. W; Kuntz, I. D. J. Comput.-Aided Mol. Des. 1992, 66, 607-628.
144. Nilakantan, R.; Bauman, N.; Venkataraghavan, R. J. Chem. Inf. Comput. Sci. 1993, 331, 79-85.
145. Good, A. C.; Ewing, T J. A.; Gschwend, D. A.; Kuntz, I. D. J. Comput.-Aided Mol. Des. 1995, 9, 1-10.
146. Sheridan, R. P.; Miller, M. D.; Underwood, D. J.; Kearsley, S. K. J. Chem. Inf. Comput. Sci. 1996, 361, 128-136.
147. Mason, J. S.; Cheney, D. L. Pac. Symp. Biocomput. 1999, 456-467.
148. McGregor, M. J.; Muskal, S. M. J. Chem. Inf. Comput. Sci. 1999, 39, 569-574.
149. Good, A. C.; Cho, S.-J.; Mason, J. S. J. Comput.-Aided Mol. Des. 2004, 18, 523-527.
150. Wold, S.; Sjöström, M.; Eriksson, L. In Encyclopedia of Computational Chemistry; John Wiley: New York, 1998, pp 2006-2021.
151. Renner, S.; Schneider, G. J. Med. Chem. 2004, 47, 4653-4664.
152. Bradley, E. K.; Beroza, P; Penzotti, J. E.; Grootenhuis, P D. J.; Spellmeyer, D. C.; Miller, J. L. J. Med. Chem. 2000, 4314, 2770-2774.
153. Lipinski, C. A.; Lombardo, F; Dominy, B. W; Feeney, P. J. Adv. Drug Deliv. Rev. 2001, 46, 3-26.
154. Lewis, R. A.; Mason, J. S.; McLay, I. M. J. Chem. Inf. Comput. Sci. 1997, 37, 599-614.
155. Xue, L.; Stahura, F L.; Godden, J. W; Bajorath, J. J. Chem. Inf. Comput. Sci. 2001, 41, 394-401.
156. Sheridan, R. P.; Nachbar, R. B.; Bush, B. L. J. Comput.-Aided Mol. Des. 1994, 83, 323-340.
157. Pearlman, R. S.; Smith, K. M. J. Chem. Inf. Comput. Sci. 1999, 391, 28-35.
158. Burden, F R. J. Chem. Inf. Comput. Sci. 1989, 29, 225-227.
159. DiverseSolutions, v4.0.5; University of Texas, Austin; distributed by Tripos, Inc. http://www.tripos.com/(accessed April 2006).
160. Pearlman, R. S.; Smith, K. M. Novel Software Tools for Chemical Diversity. In Perspective in Drug Discovery and Design; Kubinyi, H., Folkers, G., Martin, Y C., Eds.; Kluwer/Escom: Dordrecht, the Netherlands, 1998; Vols. 9/10/11, pp 339-351.
161. Lee, M. R.; Sage, C. R. Abstracts of Papers, 223rd American Chemical Society National Meeting, Orlando, FL, April 7-11, 2002, COMP-094.
162. Mason, J. S.; Beno, B. R. J. Mol. Graph. Model. 2000, 18, 438-451.
163. Gillett, V J.; Willett, P.; Bradshaw, J. J. Chem. Inf. Comput. Sci. 2003, 43, 338-345.
164. Barker, E. J.; Gardiner, E. J.; Gillett, V J.; Kitts, P.; Morris, J. J. Chem. Inf. Comput. Sci. 2003, 43, 346-356.
165. Daylight toolkit, developed and distributed by Daylight Chemical Information Systems: http://www.daylight.com/(accessed April 2006).
166. Rarey, M.; Dixon, J. S. J. Comput.-Aided Mol. Des. 1998, 12, 471-482.
167. FTREES, developed and distributed by BioSolveIT. http://www.biosolveit.de/(accessed April 2006).
168. Dixon, S. L.; Merz, K. M. J. Med. Chem. 2001, 44, 3795-3809.
169. Good, A. C. Application of 3D Molecular Similarity Index Calculations to QSAR studies. In Molecular Similarity in Drug Design; Dean, P. M., Ed.; Blackie: Glasgow, UK, 1995, pp 24-56.
170. Good, A. C.; Richards, W G. Perspect. Drug Disc. Des. 1998, 9, 321-338.
171. Carbo, R.; Besalu, E. A. Theomchem, 1998, 4511, 11-23.
172. van Geerestein, Y. J.; Perry, N. J.; Grootenhuis, P D. J.; Haasnoot, C. A. G. Tetrahedron Comput. Methodol 1992, 3, 595-613.
173. Perry, N. C.; van Geerestein, V. J. J. Chem. Inf. Comput. Sei. 1992, 32, 607-616.
174. Dean, P. M.; Chau, P-L. J. Mol. Graph. 1987, 5, 152-158.
175. Moon, J. B.; Howe, W J. Tetrahedron Comput. Methodol. 1990, 3, 697-711.
176. Good, A. C.; Hodgkin, E. E.; Richards, W G. J. Chem. Inf. Comput. Sei. 1992, 32, 188-191.
177. Carbo, R.; Domingo, L. Int. J. Quantum Chem. 1987, 32, 517-545.
178. Szabo, A., Ostland, N. S. In Modern Quantum Chemistry; Macmillan: London, 1982, pp 410-412.
179. Wild, D. J.; Willett, P. J. Chem. Inf. Comput. Sei. 1996, 36, 159-167.
180. Thorner, D. A.; Wild, D. J.; Willett, P.; Wright, P. M. Perspeet. Drug Disc. Des. 1998, 9, 301-320.
181. Good, A. C.; Richards, W G. J. Chem. Inf. Comput. Sei. 1993, 33, 112-116.
182. Grant, J. A.; Gallardo, M. A.; Pickup, B. T. J. Comput. Chem. 1996, 17, 1653-1666.
183. Mestres, J.; Rohrer, D. C.; Maggiora, G. M. J. Mol. Graph. Model. 1997,15, 114-121.
184. ROCS, developed and distributed by OpeneyeScientific Software Inc. http://www.eyesopen.com/ (accessed April 2006).
185. Rush, T S., III; Grant, A. J.; Mosyak, L.; Nicholls, A. J. Med. Chem. 2005, 485, 1489-1495.
186. Lemmen, C.; Zimmermann, M.; Lengauer, T. Perspeet. Drug Disc. Des. 2000, 20, 43-62.
187. Pitman, M. C.; Huber, W K.; Horn, H.; Kramer, A.; Rice, J. E.; Swope, W C. J. Comput.-Aided Mol. Des. 2001, 15, 587-612.
188. Kraemer, A.; Horn, H. W; Rice, J. E. J. Comput.-Aided Mol. Des. 2003, 17, 13-18.
189. Rhodes, N.; Willett, P. J. Chem. Inf. Comput. Sei. 2003, 43, 443-448.
190. Hahn, M. J. Chem. Inf Comput. Sei. 1997, 37, 80-86.
191. Putta, S.; Lemmen, C.; Beroza, P; Greene, J. J. Chem. Inf Comput. Sei. 2002, 42, 1230-1240.
192. Putta, S.; Eksterowicz, J.; Lemmen, C.; Stanton, R. J. Chem. Inf. Comput. Sei. 2003, 435, 1623-1635.
193. Engels, M. F M.; Thielemans, T; Verbinnen, D.; Tollenaere, J. P; Verbeeck, R. J. Chem. Inf Comput. Sei. 2000, 40, 241-245.
194. Bajorath, J. Nat. Rev. Drug Disc. 2002, 1, 882-894.
195. Karnachi, P. S.; Brown, F K. J. Biolmol. Screen. 2004, 9, 678-686.
196. Shanmugasundaram, V; Maggiora, G. M.; Lajiness, M. S. J. Med. Chem. 2005, 481, 240-248.
197. Smemetulskis, N. E.; Weiniger, D.; Blankley, C. J.; Yang, J. J.; Humblet, C. J. Chem. Inf. Comput. Sei. 1996, 36, 862-871.
198. Singh, S. B.; Sheridan, R. P; Fluder, E. M.; Hull, R. D. J. Med. Chem. 2001, 44, 1564-1575.
199. Klein, L. A. Sensor and Data Fusion Coneepts and Applieations, 2nd ed.; International Society for Optical Engineering: Bellingham, WA, 4.
200. Ginn, C. M. R.; Willett, P.; Bradshaw, J. Perspeet. Drug Disc. Des. 2000, 20, 11-16.
201. Charifsen, P. S.; Corkery, J. J.; Murcko, M. A. J. Med. Chem. 1999, 42, 5100-5109.
202. Wang, R.; Wang, S. J. Chem. Inf. Comput. Sei. 2001, 41, 1422-1426.
203. Salim, N.; Holliday, J. D.; Willett, P. J. Chem. Inf. Comput. Sei. 2003, 43, 435-442.
204. Wilton, D. J.; Willett, P; Lawson, K.; Mullier, G. J. Chem. Inf. Comput. Sei. 2003, 43, 469-474.
205. Harper, G.; Bradshaw, J.; Gittins, J. C.; Green, D. V S.; Leach, A. J. Chem. Inf. Comput. Sei. 2001, 41, 1295-1300.
206. Hert, J.; Willett, P.; Wilton, D. J.; Acklin, P; Azzaoui, K.; Jacoby, E.; Schuffenhauer, A. J. Chem. Inf. Comput. Sei. 2004, 44, 1177-1185.
207. Hert, J.; Willett, P.; Wilton, D. J.; Acklin, P; Azzaoui, K.; Jacoby, E.; Schuffenhauer, A. Org. Biomol Chem. 2004, 2, 3256-3266.
208. Downs, G. M.; Barnard, J. M. Clustering Methods and Their Uses in Computational Chemistry. In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; Wiley-VCH: Weinheim, Germany, 2002; Vol. 18, pp 1-40.
209. Böcker, A.; Derksen, S.; Schmidt, E.; Teckentrup, A.; Schneider, G. J. Chem. Inf Model. 2005, 45, 807-815.
210. This Java-based software is freely available: http://www.modlab.de (accessed April 2006).
211. Rusinko, A., III.; Farmen, M. W; Lambert, C. G.; Brown, P L.; Young, S. S. J. Chem. Inf. Comput. Sei. 1999, 39, 1017-1026.
212. Quinlan, J. R. In C4.5 Programs for Machine Learning, Morgan Kaufmann: San Francisco, 1992.
213. Scam has subsequently been developed into a suite of products developed and distributed by Golden Helix Inc. http://www.goldenhelix.com/ (accessed April 2006).
214. Brown, R. D.; Martin, Y C. J. Chem. Inf. Comput. Sei. 1996, 36, 572-584.
215. World Drug Index, Developed and distributed by Thomson Scientific: http://scientific.thomson.com/ (accessed April 2006).
216. Nicolaou, C. A.; Tamura, S. Y; Kelley, B. P; Bassett, S. I.; Nutt, R. F. J. Chem. Inf. Comput. Sei. 2002, 42, 1069-1079.
217. ClassPharmer, developed and distributed by Bioreason Inc. http://www.bioreason.com/ (accessed April 2006).
218. Classpharmer application presentation: http://cisrg.shef.ac.uk/shef2004/talks/CNicolaou.pdf (accessed April 2006).
219. Wagener, M.; Sadowski, J.; Gasteiger, J. Angew. Chem. Int. Ed. Engl. 1995, 34, 2674-2677.
220. Wild, D.; Blankley, C. J. J. Chem. Inf Comput. Sei. 2000, 40, 155-162.
221. Pickett, S. D.; McLay, I. M.; Clark, D. E. J. Chem. Inf. Comput. Sei. 2000, 40, 263-269.
222. Sheridan, R. P.; Kearsley, S. K. Drug Disc. Today 2002, 7, 903.
223. Good, A. C.; Hermsmeier, M. A.; Hindle, S. A. J. Comput.-Aided Mol. Des. 2004, 18, 529-536.
224. Kollman, P. Chem. Rev. 1993, 7, 2395-2417.
225. Muegge, I.; Rarey, M. Small Molecule Docking and Scoring. In Reviews in Computational Chemistry; Boyd, D. B., Lipkowitz, K. B., Eds.; Wiley-VCH: New York, 2001; Vol. 17, pp 1-60.
226. Abagyan, R.; Totrov, M. Curr. Opin. Chem. Biol. 2001, 5, 372-382.
227. Langer, T; Hoffmann, R. D. Curr. Pharm. Des. 2001, 11, 509-527.
228. Good, A. C. Curr. Opin. Drug Disc. Dev. 2001, 4, 301-307.
229. Waszkowycz, B.; Perkins, T D. J; Sykes, R. A.; Li, J. J. Res. Dev. 2001, 40, www.research.ibm.com/journal/sj/402/ (accessed April 2006).
230. Shoichet, B. K.; McGovern, S. L.; Wei, B.; Irwin, J. J. Curr. Opin. Chem. Biol. 2002, 6, 439-446.
231. Lyne, P. D. Drug Disc. Today 2002, 7, 1047-1055.
232. Taylor, R. D.; Jewsbury, P. J.; Essex, J. W. J. Comput.-Aided Mol. Des. 2002, 16, 151-166.
233. Tjma, R. Drug. Disc. Dev. com/ (accessed July 2006).
234. Kitchen, D. B.; Deconrez, H.; Furr, J. R.; Bajorath, J. Nat. Rev. Drug Disc. 2004, 3, 935-949.
235. Alvarez, J. C. Curr. Opin. Chem. Biol. 2004, 8, 365-370.
236. Shoichet, B. K. Nature 2004, 432, 862-865.
237. Barril, X.; Hubbard, R. E.; Morley, S. D. Mini Rev. Med. Chem. 2004, 13, 779-791.
238. Jansen, J. M.; Martin, E. J. Curr. Opin. Chem. Biol. 2004, 17, 359-364.
239. Krovat, E. M.; Steindl, T; Langer, T. Curr. Comp. Aided Drug Des. 2005, 1, 93-102.
240. Mohan, V; Gibbs, A. C.; Cummings, M. D.; Jaeger, E. P; DesJarlais, R. L. Curr Pharm. Des. 2005, 11, 323-333.
241. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Baht, T N.; Weissig, H.; Shindyalov, L.; Bourne, P. E. Nuel. Adds Res. 2000, 28, 235-242.
242. Sander, C.; Schneider, R. Proteins 1991, 9, 56-62.
243. Muegge, I. Med. Chem. Res. 1999, 9, 490-500.
244. Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R. J. Mol. Biol. 1997, 267, 727-748.
245. Bron, C.; Kerbosch, I. Commun. Assoe. Comput. Mach. 1973, 16, 575-577.
246. Kuhl, F S.; Crippen, G. M.; Friesen, D. K. J. Comput. Chem. 1984, 3, 524-534.
247. Ewing, T J. A.; Kuntz, I. D. J. Comput. Chem. 1997, 18, 1175-1189.
248. DOCK, developed and distributed at UCSF: http://dock.compbio.ucsf.edu/ (accessed April 2006).
249. Kuntz, I. D.; Blaney, I. M.; Oatley, S. I.; Langridge, R. L. J. Mol. Biol. 1982, 161, 269-288.
250. Kuhl, F S.; Crippen, G. M.; Friesen, D. K. J. Comput. Chem. 1984, 5, 24-34.
251. Shoichet, B. K.; Kuntz, I. D. Prot. Eng. 1993, 6, 723-732.
252. Good, A. C.; Cheney, D. L.; Sitkoff, D. F; Tokarski, J. S.; Stouch, T R.; Bassolino, D. A.; Krystek, S. R.; Li, Y; Mason, J. S.; Perkins, T. D. J. J. Mol. Graph. Model. 2003, 22, 31-40.
253. Fischer, D.; Norel, R.; Wolfson, H.; Nussinov, R. Proteins 1993, 16, 278-292.
254. Fischer, D.; Lin, S. L.; Wolfson, H. L.; Nussinov, R. J. Mol. Biol. 1995, 248, 459-477.
255. Metropolis, N.; Rosembluth, A.; Rosembluth, M.; Teller, A. J. Chem. Phys. 1953, 21, 1087-1092.
256. Abagyan, R.; Totrov, M.; Kuznetsov, D. J. Comput. Chem. 1994, 15, 488-506.
257. ICM, developed and distributed by Molsoft Inc. http://www.molsoft.com/ (accessed April 2006).
258. McMartin, C.; Bohacek, R. S. J. Comput.-Aided Mol. Des. 1997, 11, 333-339.
259. QXP, part of the FLO package, developed and distributed by Thistlesoft: http://cmcma@ix.netcom.com/ (accessed April 2006).
260. Westhead, D. R.; Clark, D. L.; Murray, C. W. J. Comput.-Aided Mol. Des. 1997, 11, 209-228.
261. Goodsell, D. S.; Olson, A. L. Proteins 1990, 8, 195-202.
262. AUTODOCK, developed and distributed by Scripps University: http://www.scripps.edu/mb/ (accessed April 2006).
263. Kirkpatrik, S.; Gelatt, C. D. J.; Vecchi, M. P. Science 1983, 220, 671-680.
264. Yue, S. Prot. Eng. 1990, 4, 177-184.
265. Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R. J. Mol. Biol 1997, 267, 727-748.
266. Gold, developed and distributed by the CCDC. http://www.ccdc.cam.ac.uk/products/ (accessed April 2006).
267. Miller, M. D.; Kearsley, S. K.; Underwood, D. I.; Sheridan, R. P. J. Comput.-Aided Mol. Des. 1994, 8, 153-174.
268. Good, A. C.; Cheney, D. L.; Sitkoff, D. F; Tokarski, J. S.; Stouch, T R.; Bassolino, D. A.; Krystek, S. R.; Li, Y; Mason, J. S.; Perkins, T. D. J. J. Mol. Graph. Model. 2003, 22, 31-40.
269. Lorber, D. M.; Shoichet, B. K. Protein Sci. 1998, 7, 938-950.
270. Thomas, B. E.; Joseph-McCarthy, D.; Alvarez, J. C. Pharmacophore-Based Molecular Docking. In Pharmacophore Perception, Development and Use in Drug Design; Guner, O. F, Ed.; International University Line: La Jolla, CA, 2000, pp 351-367.
271. Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T; Repasky, M. P; Knoll, E. H.; Shelley, M.; Perry, J. K. et al. J. Med. Chem. 2004, 477, 1739-1749.
272. GLIDE, developed and distributed by Schrodinger Inc. http://www.schrodinger.com/ (accessed April 2006).
273. Halgren, T A.; Murphy, R. B.; Friesner, R. A.; Beard, H. S.; Frye, L. L.; Pollard, W T; Banks, L. J. Med. Chem. 2004, 47, 1750-1759.
274. Zsoldos, Z.; Johnson, A. P; Simon, A.; Szabo, I.; Szabo, Z. Abstracts of Papers, 224th American Chemical Society National Meeting, Boston, MA, Aug 18-22, 2002; CINF-005.
275. EHITS is developed and distributed by Simbiosys Inc. http://www.simsbiosys.ca/ (accessed April 2006).
276. Muegge, I. Med. Chem. Res. 1999, 9, 490-500.
277. Najmanovich, R.; Kuttner, I.; Sobolev, V. Proteins 2000, 39, 261-268.
278. Leach, A. R. J. Mol. Biol. 1994, 235, 345-356.
279. Wasserman, Z. R.; Hodge, C. N. Proteins 1996, 24, 227-237.
280. Knegtel, R. M. A.; Kuntz, I. D.; Oshiro, C. M. J. Mol. Biol. 1997, 266, 424-440.
281. Broughton, H. B. J. Mol. Graph. Model 2000, 18, 247-257.
282. Cavasotto, C.; Abagyan, A. J. Mol. Biol. 2004, 337, 209-225.
283. Claussen, H.; Buning, C.; Rarey, M.; Lengauer, T. J. Mol. Biol. 2001, 308, 377-395.
284. FlexE, developed and distributed by BioSolveIT. http://www.biosolveit.de/FlexE, and Tripos Inc. http://www.tripos.com/ (accessed April 2006).
285. Schnecke, V; Swanson, C. A.; Getzoff, E. D.; Tainer, J. A.; Kuhn, L. A. Protdns 1998, 33, 74-87.
286. Barril, X.; Morley, S. D. J. Med. Chem. 2005, 48, 4432-4443.
287. Drug-Reeeptor Thermodynamics: Introduction and Applications; Raffa, R. B., Ed.; John Wiley: Chichester, UK, 2001.
288. Gohlke, H.; Klebe, G. Angew. Chem. Int. Ed. Engl. 2002, 41, 2644-2676.
289. Boehm, H.-J. Prediction of Non-Bonded Interactions in Drug Design. In Methods and Principles in Medidnal Chemistry; Mannhold, R.; Kubinyi, H.; Folkers, G., Eds.; Vol. 19, pp 3-20.
290. Brooijmans, N.; Kuntz, I. D. Annu. Rev. Biophys. Biol. Struct. 2003, 32, 335-373.
291. Muegge, I.; Enyedy, I. In Computational Medicinal Chemistry for Drug Discovery; Bultinck, P, de Winter, H., Langenaeker, W, Tollenaere, J. P, Eds.; Marcel Dekker: New York, 2004, pp 405-436.
292. Krovat, E. M.; Steindl, T; Langer, T. Curr. Comput. Aided Drug Des. 2005, 1, 93-102.
293. Nielsen, D. L.; Aadal, P; Hedstroem, M.; Norden, B. Curr. Comput. Aided Drug Des. 2005, 1, 275-306.
294. Muegge, I. J. Med. Chem. ACS.
295. Cole, J. C.; Nissink, J.; Willem, M.; Taylor, R. Virtual Screen. Drug Disc. 2005, 14, 379-415.
296. Weiner, S.; Kollman, P. A.; Nguyen, D. T.; Case, D. A. J. Comput. Chem. 1986, 7, 230-239.
297. Meng, E. C.; Shoichet, B. K.; Kuntz, I. D. J. Comput. Chem. 1992, 13, 505-524.
298. Vieth, M.; Hirst, J. D.; Kolinski, A.; Brooks, C. L., III. J. Comput. Chem. 1998, 14, 1612-1622.
299. Joseph-McCarthy, D. Pharm. Ther. 1999, 84, 179-191.
300. Weber, P C.; Pantoliano, M. W; Simons, D. M.; Salemme, F R. J. Am. Chem. Soc 1994, 116, 2717-2727.
301. Honig, B.; Nicholls, A. Science 1995, 268, 1144-1149.
302. Zou, X.; Sun, Y.; Kuntz, I. D. J. Am. Chem. Soc. 1999, 121, 8033-8043.
303. Still, W G.; Tempczyk, A.; Hawley, R. G.; Hendrickson, T. J. Am. Chem. Soc. 1990, 112, 6127-6129.
304. Kalyanaraman, G.; Bernacki, K.; Jacobson, M. R. Biochemistry 2005, 44, 2059-2071.
305. Kellogg, G. E.; Fornabaio, M.; Spyrakis, E; Lodola, A.; Gozzini, R; Mozzarelli, A.; Abraham, D. J. J. Mol. Graph. Model. 2004, 22, 479-486.
306. Eldridge, M. D.; Murray, G. W; Auton, T. R.; Paolini, G. V; Mee, R. P. J. Comput.-Aided Mol. Des. 1997, 11, 425-445.
307. Murray, G. W; Auton, T R.; Eldridge, M. D. J. Comput.-Aided Mol. Des. 1998, 12, 503-519.
308. Gscore, part of SYBYL, developed and distributed by Tripos Inc. http://www.tripos.com/ (accessed April 2006).
309. Wang, R.; Liu, L.; Lai, L.; Tang, Y. J. Mol. Model. 1998, 4, 379-394.
310. Head, R. D.; Smythe, M. L.; Oprea, T I.; Waller, G. L.; Green, S. M.; Marshall, G. R. J. Am. Chem. Soc. 1996, 118, 3959-3969.
311. Jain, A. N. J. Comput.-Aided Mol. Des. 1996, 10, 427-440.
312. Krammer, A.; Kirchhoff, R D.; Jiang, X.; Venkatachalam, G. M.; Waldman, M. J. Mol. Graph. Model. 2005, 23, 395-407.
313. Glide XP, developed and distributed by Scrodinger Inc. http://www.schrodinger.com/ (accessed April 2006).
314. Sippl, M. J. Curr. Opin. Struct. Biol. 1995, 5, 229-235.
315. Sippl, M. J. J. Mol. Biol. 1990, 213, 859-883.
316. Verkhivker, G.; Appelt, Κ.; Freer, S. T; Villafranca, J. E. Protein Eng. 1995, 8, 677-691.
317. Pickett, S. D.; Sternberg, M. J. J. Mol. Biol. 1993, 231, 825-839.
318. Wallqvist, A.; Jernigan, R. L.; Covell, D. G. Protein Sei. 1995, 4, 1881-1903.
319. DeWitte, R. S.; Shakhnovich, E. I. J. Am. Chem. Soc. 1996, 118, 11733-11744.
320. Mitchell, J. B. O.; Laskowski, R. A.; Alex, A.; Thornton, J. M. J. Comput. Chem. 1999, 20, 1165-1176.
321. McDonald, I. Κ.; Thornton, J. M. J. Mol. Biol. 1994, 238, 777-793.
322. Mitchell, J. B. O.; Laskowski, R. A.; Alex, A.; Forster, M. J.; Thornton, J. M. J. Comput. Chem. 1999, 20, 1177-1185.
323. Muegge, I.; Martin, Y. G. J. Med. Chem. 1999, 42, 791-804.
324. Muegge, I. J. Comput. Chem. 2001, 22, 418-425.
325. Gohlke, H.; Hendlich, M.; Klebe, G. J. Mol. Biol. 2000, 205, 337-356.
326. Hendlich, M. Acta Crystallogr. Sect. D 1998, 54, 1178-1182.
327. Muryshev, A. E.; Tarasov, D. N.; Butygin, A. V; Butygina, O. Y.; Aleksandrov, A. B.; Nikitin, S. M. J. Comput.-Aided Mol. Des. 2003,17, 597-605.
328. Zhang, C.; Liu, S.; Zhu, Q.; Zhou, Y. J. Med. Chem. 2005, 48, 2325-2335.
329. Yang, J.-M.; Chen, Y.-E; Shen, T-W; Kristal, B. S.; Hsu, D. E. J. Chem. Info. Model. 2005, 45, 1134-1146.
330. Stahl, M. Perspeet. Drug Disc. Des. 2000, 20, 83-98.
331. Wang, R.; Lu, Y.; Wang, S. J. Med. Chem. 2003, 46, 2287-2303.
332. Bissantz, C.; Folkers, G.; Rognan, D. J. Med. Chem. 2000, 43, 4759-4767.
333. Stahl, M.; Rarey, M. J. Med. Chem. 2001, 44, 1035-1042.
334. Marsden, P. M.; Puvanendrampillai, D.; Mitchell, J. B. O.; Glen, R. C. Org. Biomol. Chem. 2004, 2, 3267-3273.
335. Klon, A. E.; Glick, M.; Davies, J. W. J. Med. Chem. 2004, 47, 4356-1359.
336. Xing, L.; Hodgkin, E.; Liu, Q.; Sedlock, D. J. Comput.-Aided Mol. Des. 2004, 18, 333-344.
337. Gehlhaar, D. K.; Verkhivker, G. M.; Rejto, P. A.; Sherman, C. J.; Fogel, L. J.; Freer, S. T. Chem. Biol. 1995, 2, 317-324.
338. Smith, R.; Hubbard, R. E.; Gschwend, D. A.; Leach, A. R.; Good, A. C. J. Mol. Graph. Model. 2003, 22, 41-53.
339. Davis, A. M.; Teague, S. J.; Kleywegt, G. J. Angew. Chem. Int. Ed. Engl. 2003, 42, 2718-2736.
340. Nissink, J.; Willem, M.; Murray, C.; Hartshorn, M.; Verdonk, M. L.; Cole, J. C.; Taylor, R. Proteins: Struct. Funct. Genet. 2002, 49, 457-471.
341. Hu, L.; Benson, M. L.; Smith, R. D.; Lerner, M. G.; Carlson, H. A. Proteins: Struct. Funct. Bioinform. 2005, 60, 333-340.
342. Graves, A. P.; Brenk, R.; Shoichet, B. K. J. Med. Chem. 2005, 48, 3714-3728.
343. Cole, J. G.; Murray, G. W; Nissink, J. W M.; Taylor, R. D.; Taylor, R. Proteins: Struct. Funct. Bioinform. 2005, 60, 325-332.
344. Yang, J. M.; Shen, T. W. Proteins: Struct. Funct. Bioinform. 2005, 59, 205-220.
345. Gruneberg, S.; Wendt, B.; Klebe, G. Angew. Chem. Int. Ed. Engl. 2001, 40, 389-393.
346. Honma, T. Structure-Based Design of Potent and Selective Cdk4 Inhibitors Protein Crystallography in Drug Discovery. In Babine, R. E., Abdel-Meguid, S. S., Eds.; John Wiley: New York, 2004; http://www3.interscience.wiley.com/cgi~bin/ (accessed April 2006).
347. Wu, J. H.; Batist, G. Anti-Cancer Drug Des. 2001, 16, 129-133.
348. Schapira, M.; Raaka, B. M.; Samuels, H. H. BMC Struct. Biol. 2001, 1, 1-13.
349. Kelly, T M. Biochim. Biophys. Acta 2001, 1545, 67-77.
350. Perola, E.; Xu, K.; Kollmeyer, T M. J. Med. Chem. 2000, 43, 401-108.
351. Klebe, G. J. Med. Chem. 2004, 47, 5381-5392.
352. PRO_LEADS Docking presentation, http://www.lib.uchicago.edu/cinf/ (accessed April 2006).
353. Vangrevelinghe, E.; Zimmermann, K.; Schoepfer, J.; Portmann, R.; Fabbro, D.; Furet, P. J. Med. Chem. 2003, 46, 2656-2662.
354. Doman, T N.; McGovern, S. L.; Witherbee, B. J.; Kasten, T. P.; Kurumbail, R.; Stallings, W C.; Connolly, D. T; Shoichet, B. K. J. Med. Chem. 2002, 45, 2213-2221.
355. Brenk, R.; Naerum, L.; Gradier, U.; Gerber, H.-D.; Garcia, A. G.; Reuter, G. K.; Stubbs, M. T; Klebe, G. J. Med. Chem. 2003, 46, 1133-1143.
356. Oshiro, C.; Bradley, E. K.; Eksterowicz, J.; Evensen, E.; Lamb, M. L.; Lanctot, J. K.; Putta, S.; Stanton, R.; Grootenhuis, P. D. J. J. Med. Chem. 2004, 47, 764-767.
357. Evers, A.; Klabunde, T. J. Med. Chem. 2005, 48, 1088-1097.
358. Evers, A.; Gohlke, H.; Klebe, G. J. Mol. Biol. 2003, 334, 327-345.