Pharmacophore Model Generation Software Tools

Pharmacophores and Pharmacophore Searches

Volumn , Issue , 2006, Pages 15-47

  Poptodorov, Konstantin ^a   Luu, Tien ^a   Hoffmann, Rémy D ^b  

^a Accelrys Limited UK   (United Kingdom)

^b Parc Club Orsay Universite   (France)

Author keywords

Automated pharmacophore generation methods; Generation software tools; Molecular alignments; Other methods; Pharmacophore approaches; Pharmacophore modeling; Pharmacophores

Indexed keywords

COMPUTER SOFTWARE; MOLECULAR ORIENTATION;

GENERATION METHOD; OTHER METHODS; PHARMACOPHORE MODELING; PHARMACOPHORES;

PHARMACODYNAMICS;

EID: 84952939473     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/3527609164.ch2     Document Type: Chapter

References (107)

1. Ehrlich, P., Ber. Dtsch. Chem. Ges., 1909, 42, 17.
2. Guner, O.F., Curr. Top. Med. Chem., 2002, 2, 13121-1332.
3. Mason, J.S., Good, A.C., Martin, E. J., Curr. Pharm. Des., 2001, 7, 567-597.
4. McGregor, M. J., Muskal S.M., J. Chem. Inf. Comput. Sci., 1999, 39, 569-574.
5. McGregor, M. J., Muskal, S.M., J. Chem. Inf. Comput. Sci., 2000, 40, 117-125.
6. Martin, E.J., Hoeffel, T.J., J. Mol. Graph. Model., 2000, 18, 383-403.
7. Cerius 2 . Accelrys Software, San Diego, CA; http://www.accelrys.com/.
8. Tuplets. Tripos, St. Louis, MO; http:// www.tripos.com/
9. Van Drie, J.H., Weininger, D., Martin, Y.C., J. Comput.-Aided Mol. Des., 1989, 3, 225-251.
10. VanDrie, J.H., J. Comput.-Aided Mol. Des., 1996, 10, 623.
11. VanDrie, J.H., J. Comput.-Aided Mol. Des., 1997, 11, 39-52.
12. Van Drie, J.H., J. Chem. Inf. Comput. Sci., 1997, 37, 38-42.
13. Van Drie, J.H., Nugent, R.A., SAR QSAR Environ. Res., 1998, 9, 1-21.
14. Snyder, J.P., Rao, S.N., Koehler, K.F., Vedani, A., Pellicciari, R., in Trends in QSAR and Molecular Modeling, C.G.Wermuth, Y. Rival (eds.). 1993, Elsevier: Amsterdam. p. 367-403.
15. Finn, P.W., Karraki, L.E., Latombe, J.-C., Motwani, R., Shelton, C., Venkatasubra- manian, S., Yao, A., RAPID: randomized pharmacophore identification for drug design, in: Proc of the 3rd annual sympo- sium on computational geometry, Nice, France, ACM Press, p. 324-333.
16. SCREEN. http://www.jchem.com/in- dex.html?content=doc/user/Screen.html.
17. Good, A.C., Cheney, D.L., J. Mol. Graph. Model., 2003, 22, 23-30.
18. Dammkoehler, R.A., Karasek, S.F., Shands, E.F.B., Marshall, G.R, J. Com- put.-Aided Mol. Des., 1995, 9, 491-499.
19. Marshall, G.R., Barry, C.D., Bosshard, H.D., Dammkoehler, R.D., Dunn, D.A., Comput.-Assist. Drug Des., 1979, 112, 205-222.
20. Klebe, G., in 3D QSAR in Drug Design. Theory, Methods and Applications,H.Ku- binyi (ed.). ESCOM, Leiden, 1993, pp. 173-199.
21. Bures, M.G., in: Practical Application of Computer-Aided Drug Design, P.S. Charif- son (ed.). Marcel Dekker, New York, 1997, pp. 39-72.
22. Melani, F., Gratteri, P., Adamo, M., Bo- naccini, C., J. Med. Chem., 2003, 46, 1359-1371.
23. Brint, A.T., Willett, P., J. Comput.-Aided Mol. Des., 1989, 2, 311-320.
24. Gardiner, E. J., Artymiuk, P. J., Willett, P., J. Mol. Graph. Model., 1997, 15, 245-253.
25. Goodford, P., J. Med. Chem., 1985, 28, 849-857.
26. Nissink, J.W.M., Verdonk, M.L., Kroon, J. Mietzner, T., Klebe, G., J. Comput. Chem., 1997, 18, 638-645.
27. Barbany, M., Gutiérrez-de-Terán, H. Sanz, F., Villà-Freixa, J., Proteins: Struct. Funct. Bioinf., 2004, 56, 585-594.
28. Mestres, J., Rohrer, D.C., Maggiora, G.M., J. Comput. Chem., 1997, 18, 934- 954.
29. Pitman, M.C., Huber, W.K., Horn, H., Krämer, A., Rice, J.E. Swope, W.C., J. Comput.-Aided Mol. Des., 2001, 15, 587- 612.
30. Mills, J.E. J., de Esch, I. J.P., Perkins, T.D. J., Dean, P.M., J. Comput.-Aided Mol. Des., 2001, 15, 81-96.
31. Hurst, T., J. Chem. Inf. Comput. Sci., 1994, 34, 190-196.
32. Kirkpatrick, S., Gelatt, C.D., Jr., Vecchi, M,P., Science, 1983, 220, 671-680.
33. Cerny, V., J. Optim. Theory Appl., 1985, 45, 41-51.
34. Spendley, W., Hext, G.R., Himsworth, F.R., Technometrics, 1962, 441-461.
35. Jones, G., Willett, P., Glen, R.C., J. Com- put.-Aided Mol. Des., 1995, 9, 532-549.
36. Handschuh, S., Wagener, M., Gasteiger, J., J. Chem. Inf. Comput. Sci., 1998, 38, 220-232.
37. Smellie, A., Teig, S., Towbin P., J. Com- put. Chem., 1994, 16, 171-187.
38. Marshall, G.R., Barry, C.D., Bosshard, H.E., Dammkoehler, R.A., Dunn, D.A., in Computer-Assisted Drug Design,E.C. Olson, R.E. Christoffersen (eds.) Ameri- can Chemical Society, Washington, DC, 1979, p. 205-226.
39. Guner, O.F. (ed.), Pharmacophore Percep- tion, Development and Use in Drug Design. IUL Biotechnology Series, Vol. 1. IUL, La Jolla, CA, 2000.
40. Kugori, Y., Güner, O.F., Curr. Med. Chem., 2001, 8, 1035-1055.
41. Golender, V., Vesterman, B, Vorpagel, E., APEX-3D Expert System for Drug Design; http://www.netsci.org/Science/Comp- chem/feature09.html.
42. Triballeau, N., Bertrand, H.-O., Acher, F., in Pharmacophores and Pharmacophore Searches, T. Langer and R. Hoffmann (eds.), Wiley-VCH, Weinheim, 2006, p. 325-362.
43. Triballeau, N., Acher, F., Brabert, I., Pin J.-P., Bertrand, H.-O., J. Med. Chem., 2005, 48, 2534-2547.
44. Krovat, E.M., Fruhwirth, K.H., Langer, T., J. Chem. Inf. Model., 2005, 45, 146- 159.
45. Lengauer, T., Lemmen, C., Rarey, M., Zimmermann, M., Drug Discov. Today, 2004, 9, 27-34.
46. Rollinger, J.M., Haupt, S., Stuppner, H., Langer, T., J. Chem. Inf. Comput. Sci., 2004, 44, 480-488.
47. Steindl, T.M., Crump, C.E., Hayden, F.G., Langer, T., J. Med. Chem., 2005, 48, 6250-6260.
48. Good, A.C., Cho, S. J., Mason, J.S., J. Comput.-Aided Mol. Des., 2004, 7, 523- 527.
49. Christmann-Franck, S., Bertrand, H.-O., Goupil-Lamy, A., der Garabedian, P.A., Mauffret, O., Hoffmann, R., Fermand- jian, S., J. Med. Chem., 2004,47, 6840- 6853.
50. Evers, A., Hessler, G., Matter, H., Kla- bunde, T., J. Med. Chem., 2005, 48, 5448-5465.
51. Klabunde, T., Hessler, G., ChemBiochem., 2002, 3, 928-944.
52. Sybyl. Tripos, St. Louis, MO; http://www.tripos.com/.
53. Connolly Martin, Y., in Pharmacophore Perception, Development and Use in Drug Design, O. Guner (ed.). IUL Biotechnol- ogy Series, Vol. 1. IUL, La Jolla, CA, 2000, p. 49-68.
54. Patel, Y., Gillet, V. J., Bravi, G., Leach, A.R., J. Comput.-Aided Mol. Des., 2002, 16, 653-681.
55. DISCOtech. Tripos, St. Louis, MO; http://www.tripos.com/.
56. Unity. Tripos, St. Louis, MO; http://www.tripos.com/.
57. Jung, D.F., J., Gund, T.M., J. Comput. Chem., 2004, 25, 1385-1399.
58. Jones, G., Willett, P., Glen, R.C., Leach, A.R., Taylor R., J. Mol. Biol., 1997, 267, 727-748.
59. GASP. Tripos, St. Louis, MO; http://www.tripos.com/.
60. Jones, G., Willett, P., Glen, R.C., in Pharmacophore Perception, Development and Use in Drug Design, O. Guner (ed.). IUL Biotechnology Series, Vol. 1. IUL, La Jolla, CA, 2000, p. 87-106.
61. Yuan, H., Kozikowski, A.P., Petukhov, P.A., J. Med. Chem., 2004, 47, 6137- 6143.
62. GALAHAD. Tripos, St. Louis, MO; http://www.tripos.com/.
63. Cottrell, S. J., Gillet, V. J., Taylor, R., Wil- ton, D., J.Comput.-Aided Mol. Des., 2004, 18, 665-682.
64. Richmond, N. J., Willet, P., Clark, R.D., J. Mol. Graph. Model., 2004, 23, 199-209.
65. GALAHAD, Tripos, St. Louis, MO; http://www.tripos.com/data/SYBYL/ GALAHAD_9-7-05.pdf.
66. Hurst, T., J. Chem. Inf. Comput. Sci., 1994, 34, 190-196.
67. Catalyst. Accelrys Software, San Diego, CA; http://www.accelrys.com.
68. Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D. J., Swaminathan, S., J. Comput. Chem., 1983, 4, 187-217.
69. Smellie, A., Kahn, S.D, Teig, S.L., J. Chem. Inf. Comput. Sci., 1995, 35, 285-294.
70. Smellie, A.K., Kahn, S.D, Teig, S.L, J. Chem. Inf. Comput. Sci., 1995, 35, 295-304.
71. Barnum, D., Greene, J, Smellie, A., Sprague, P., J. Chem. Inf. Comput. Sci., 1996, 36, 563-571.
72. Maynard, A. J., HypoGenRefine and Hi- pHopRefine: pharmacophore refinement using steric information from inactive compounds. Presented at the ACS Na- tional Meeting, Spring, 2004.
73. Toba, S., Srinivasan, J., Maynard, A. J., Sutter, J., J. Chem. Inf. Model., 2005, 46, 728-735.
74. Sprague, P., Hoffmann, R., in Computer- Assisted Lead Finding and Optimization, B.T. H. van de Waterbeemd, G. Folkers (eds.). Wiley-VCH, Weinheim, 1997, pp. 225-240.
75. Hahn, M., J. Chem. Inf. Comput. Sci., 1997, 37, 80-86.
76. Hahn, M., J. Med. Chem., 1995, 38, 2080-2090.
77. Hahn, M., Rogers, D., J. Med. Chem., 1995, 38, 2091-2102.
78. FlexS. Tripos, St. Louis, MO; http://www.tripos.com/.
79. Lemmen, C., Lengauer, T., Klebe, G., J. Med. Chem., 1998, 41, 4502-4520.
80. ROCS. OpenEye Scientific Software, Santa Fe, NM. http://www.eyesopen.com.
81. Grant, J.A., Gallardo, M.A., Pickup, B., J. Comput. Chem., 1996, 17, 1653.
82. Phase. Schrödinger, Portland, OR; http://www.schrodinger.com/.
83. Maestro. Schrödinger, Portland; OR, http://www.schrodinger.com/.
84. LigPre. Schrödinger, Portland; OR, http://www.schroedinger.com/.
85. Maestro. Schrödinger, Portland; OR, http://www.schroedinger.com/.
86. Jorgensen, W.L., Maxwell, D.S. Tirado- Rives, J., J. Am.Chem. Soc., 1996, 118, 11225-11236.
87. Halgren, T.A., J. Comput. Chem., 1998, 17, 490-519.
88. Molecular Operating Environment. Chemi- cal Computing Group, Montreal, QC; http://www.chemcomp.com/.
89. CCG: Methodology Development and Deployment; http://www.chemcomp.- com/software-mdd.htm.
90. SVL Exchange; http://svl.chemcomp.- com/.
91. Lin, A., Overview of pharmacophore appli- cations in MOE; http://www.chemcomp.com/journal/ph4.htm.
92. Labute, P., Flexible alignment of small molecules; http://www.chemcomp.com/ journal/malign.htm.
93. Clark, R.D., Leonard, J.M., Strizhev, A., in Pharmacophore Perception, Development and Use in Drug Design, O. Guner (ed.). IUL Biotechnology Series, Vol. 1. IUL, La Jolla, CA, 2000, p. 151-167.
94. Livingstone, D., Data Analysis for Che- mists. Oxford University Press, Oxford, 1995.
95. eXtended Electron Distribution (XED). Cresset BioMolecular Discovery, Letch- worth; http://www.cresset-bmd.com/.
96. Vinter, J.G., J. Comput.-Aided Mol. Des., 1994, 8, 653-668.
97. Chessari, G., Hunter, C.A., Low, C.M., Packer, M. J., Vinter, J.G., Zonta, C., Chem. Eur. J., 2002, 8, 2860-2867.
98. Apaya, R.P., Lucchese, B., Price, S.L., Vinter, J.G., J Comput.-Aided Mol. Des., 1995, 9, 33-43.
99. Boström, J., J. Comput.-Aided Mol. Des., 2001, 15, 1137-1152.
100. Vinter, J.G., Trollope, K. I., J. Comput.- Aided Mol. Des., 1995, 9, 297-307.
101. FieldPrint TM. Cresset Biomolecular Dis- covery, Letchworth; http://www.cresset- bmd.com/.
102. Cresset Database, Cresset BioMolecular Discovery, Letchworth; http://www.cressetbmd.com/technology5.html.
103. Sittampalam, G.S., Kahl, S.D., Janzen, W.P., Curr. Opin. Chem. Biol., 1997, 1, 384-391.
104. Chen, X., Rusinko, A., Tropsha, A., Young S., J. Chem. Inf. Comput. Sci., 1999, 39, 887-896.
105. THINK. Treweren Consultants, Ever- sham; http://www.treweren.com/.
106. Rarey, M., Dixon, J.S., J. Comput.-Aided Mol. Des., 1998, 12, 471-490.
107. Sternberg, M. J.E., Muggleton, S.H., QSAR Comb. Sci., 2003, 22, 527-532.