Novel semi-automated methodology for developing highly predictive QSAR models: Application for development of QSAR models for insect repellent amides

Journal of Molecular Modeling

Volumn 13, Issue 1, 2007, Pages 179-208

  Bhonsle, Jayendra B ^a   Bhattacharjee, Apurba K ^a   Gupta, Raj K ^b  

^a Division of Neuropsychiatry   (United States)

^b Research Plans and Programs   (United States)

Author keywords

3D QSAR; Bioactive conformer mining; Cerius2 scripts; Insect repellents

Indexed keywords

AMIDE; INSECT REPELLENT;

ARTICLE; AUTOMATION; BIOLOGICAL ACTIVITY; CHEMICAL ANALYSIS; CHEMICAL STRUCTURE; CLUSTER ANALYSIS; COMPUTER PREDICTION; COMPUTER PROGRAM; CONFORMATION; CORRELATION ANALYSIS; DATA ANALYSIS; GEOMETRY; INTERNAL VALIDITY; MOLECULAR MECHANICS; MOLECULAR MIMICRY; MOLECULAR MODEL; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; QUANTUM MECHANICS; REGRESSION ANALYSIS; SEQUENTIAL ANALYSIS;

ALGORITHMS; AMIDES; AUTOMATION; CHEMISTRY, PHARMACEUTICAL; CLUSTER ANALYSIS; DRUG DESIGN; INSECT REPELLENTS; LEAST-SQUARES ANALYSIS; MODELS, CHEMICAL; MODELS, MOLECULAR; MODELS, STATISTICAL; MOLECULAR CONFORMATION; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; REGRESSION ANALYSIS; SOFTWARE;

INSECTA;

EID: 37349047417     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-006-0132-0     Document Type: Article

References (75)

1. Hansch C (1969) Acc Chem Res 2:232-239
2. Cramer RD III, Patterson DE, Bunce JD (1988) J Am Chem Soc 110:5959-5967
3. Hopfinger AJ, Burke BJ (1990) In: Johnson MA, Maggiora GM (eds) Molecular shape analysis: A formalism to quantitatively establish spatial molecular similarity. Wiley, New York, pp 173-209
4. Klebe G (1998) Perspectives in drug discovery and design. 12/13/14:87-104
5. Jain AN, Dietterich TG, Lathrop RH, Chapman D, Critchlow RE Jr, Bauer BE, Webster TA, Lozano-Perez T (1994) J Comput-Aid Mol Des 8:635-652
6. Doweyko AM (1991) J Math Chem 7:273-285
7. Wiener H (1947) J Am Chem Soc 69:17-20
8. Bonchev D (1983) Chemometrics series, vol 5. Information theoretic indices for characterization of chemical structures, p 249
9. Hosoya H (1971) Bull Chem Soc Jpn 44:2332-2339
10. Kier LB, Hall LH (1976) Medicinal chemistry, vol 14. Molecular connectivity in chemistry and drug research. Academic, New York, p 257
11. Kier LB (1985) Quant Struct-Act Relat 4:109-116
12. Kier LB, Hall LH, Frazer JW (1991) J Math Chem 7:229-241
13. Balaban AT (1982) Chem Phys Lett 89:399-404
14. Bonchev D, Mekenyan O, Trinajstic N (1981) J Comput Chem 2:127-148
15. Marsili M, Gasteiger J (1981) Croat Chem Acta 53:601-614
16. Rohrbaugh RH, Jurs PC (1987) Anal Chim Acta 199:99-109
17. Stanton DT, Jurs PC (1990) Anal Chem 62:2323-2329
18. Kharkar PS, Desai B, Gaveria H, Varu B, Loriya R, Naliapara Y, Shah A, Kulkarni VM (2002) J Med Chem 45:4858-4867
19. Drew MGB, Wilden GRH, Spillane WJ, Walsh RM, Ryder CA, Simmie JM (1998) J Agricult Food Chem 46:3016-3026
20. Hirashima A, Rafaeli A, Gileadi C, Kuwano E (1999) Bioorg Med Chem 7:2621-2628
21. Hasegawa K, Arakawa M, Funatsu K (2000) Chemom Intell Lab Syst 50:253-261
22. Hopfinger AJ, Wang S, Tokarski JS, Jin B, Albuquerque M, Madhav PJ, Duraiswami C (1997) J Am Chem Soc 119:10509-10524
23. Hasegawa K, Arakawa M, Funatsu K (2003) Comput Biol Chem 27:211-216
24. Vedani A, McMasters DR, Dobler M (2000) Quant Struct-Act Relat 19:149-161
25. Appell M, Dunn WJ, Reith MEA, Miller L, Flippen-Anderson JL (2002) Bioorg Med Chem 10:1197-1206
26. Xiao Y-D, Hammond PS, Harris R, Schmitt JD, Klucik J (2004) J Med Chem 47:6831-6839
27. Sulea T, Kurunczi L, Oprea TI, Simon Z (1998) J Comput-Aid Mol Des 12:133-146
28. Bhonsle JB, Wang Z-X, Tamamura H, Fujii N, Peiper SC, Trent JO (2005) QSAR & Combinat Sci 24:620-630
29. Accelrys Software Inc (2005) Cerius2 Modeling Environment, Release 4.9. San Diego, CA, USA
30. Brewste D (2001) BioMed J 323:289
31. Bock GR, Cardew G (1996) Symposium on Olfaction in Mosquito-Host Interactions, held in Collaboration with the World Health Organization at the Ciba Foundation, London, 31 October-2 November 1995. In: Ciba Found Symp 200. p 331
32. Davis EE, Bowen MF (1994) J Am Mosquito Control 10:316-325
33. Davis EE (1985) J Med Entomol 22:237-243
34. McIver SB (1981) J Med Entomol 18:357-361
35. Justice RW, Biessmann H, Walter MF, Dimitratos SD, Woods DF (2003) BioEssays 25:1011-1020
36. Rao SS, Rao KM, Ramachandran PK (1988) J Sci & Indust Res 47:722-735
37. McGovern TP, Schreck CE, Jackson J (1984) Mosquito News 44:11-16
38. Skinner WA, Johnson HL (1980) Med Chem 11:277-305
39. Sugawara R, Tominaga Y, Suzuki T (1977) Insect Biochem 7:483-485
40. Wright RH (1975) Sci Am 233:104-111
41. Suryanarayana MVS, Pandey KS, Prakash S, Raghuveeran CD, Dangi RS, Swami RV, Rao KM (1991) J Pharm Sci 80:1055-1057
42. Ma D, Bhattacharjee AK, Gupta RK, Karle JM (1999) Am J Trop Med Hyg 60:1-6
43. Bhattacharjee AK, Gupta RK, Ma D, Karle JM (2000) J Mol Recognit 13:213-220
44. Bhattacharjee AK, Dheranetra W, Nichols DA, Gupta RK (2005) QSAR & Combinat Sci 24:593-602
45. Marsili M, Gasteiger J (1981) Stud Phys Theor Chem 16:56-67
46. Mayo SL, Olafson BD, Goddard WAI (1990) J Phys Chem 94:8897-8909
47. Golbraikh A, Tropsha A (2002) Molecular Diversity 5:231-243
48. Accelrys Software Inc (2005) Performing a conformational analysis. In: Cerius2, version 4.10L. Conformational Search & Analysis Manual, vol San Diego, CA, USA, p 49
49. Bhonsle JB (2005) Cerius2_ConfSrchAndAnalysis
50. Accelrys Software Inc (2005) Genetic Function Approximation. In: Cerius2, version 4.10. QSAR Manual, vol San Diego, CA, p 237
51. Accelrys Software Inc (2005) In: Cerius2, version 4.10. QSAR Manual, vol San Diego, CA, p 34
52. Accelrys Software Inc (2005) Theory: Statistical Methods. In: Cerius2, version 4.10. QSAR Manual, vol San Diego, CA, p 33
53. Bro R (1996) J Chemomet 10:47-61
54. Hasegawa K, Arakawa M, Funatsu K (1999) Chemom Intell Lab Syst 47:33-40
55. Bhonsle JB (2005) Cerius2_QSARModel_computationScript
56. Accelrys Software Inc (2005) Catalyst, version 4.10. San Diego, California, USA
57. Bhonsle JB (2005) Cerius2_confAlignmentScript
58. Ghose AK, Crippen GM (1986) J Comput Chem 7:565-577
59. Ghose AK, Crippen GM (1987) J Chem Inf Comput Sci 27:21-35
60. Kier LB, Hall LH (1992) The electrotopological state index: An atom-centered index for QSAR. Academic, London, UK, pp 205
61. Hall LH, Kier LB (1991) Rev Comput Chem 2:367-422
62. Hill TL (1960) An introduction to statistical thermodynamics. Addison-Wesley Publishing Co, Reading, Massachusetts, p 508
63. Dewar MJS, Thiel W (1977) J Am Chem Soc 99:4907-4917
64. Richon AB, Young SS (1997) An introduction to QSAR methodology. Network Science Corporation, Saluda, NC
65. L'Heureux PJ, Carreau J, Bengio Y, Delalleau O, Yue SY (2004) J Comput-Aid Mol Des 18:475-482
66. Olah M, Bologa C, Oprea TI (2004) J Comput-Aid Mol Des 18:437-449
67. Sutter JM, Dixon SL, Jurs PC (1995) J Chem Inf Comput Sci 35:77-84
68. Zheng W, Tropsha A (2000) J Chem Inf Comput Sci 40:185-194
69. Yao SW, Lopes VHC, Fernandez F, Garcia-Mera X, Morales M, Rodríguez-Borges JE, Cordeiro MNDS (2003) Bioorganic & Medicinal Chemistry 11:4999-5006
70. Tripos Inc (2003) Sybyl Molecular Modeling System, version 6.9.1. St. Louis, MO, USA
71. Johnson HL, Tsakotellis P, Skinner WA, Skidmore D, Maibach HI (1971) J Pharm Sci 60:84-89
72. Sandler BH, Nikonova L, Leal WS, Clardy J (2000) Chem Biol 7:143-151
73. McKenna MP, Hekmat-Scafe DS, Gaines P, Carlson JR (1994) J Biol Chem 269:16340-16347
74. Pikielny CW, Hasan G, Rouyer F, Rosbash M (1994) Neuron 12:35-49
75. Beyer WH (1985) CRC Handbook of Tables for Probability and Statistics, 2nd edn. CRC Press Inc, Boca Raton, FL, pp 305-310