49. Kier LB (1967) Molecular orbital calculation of preferred conformations of acetylcholine,
muscarine, and muscarone. Mol Pharmacol 3:487–494
50. Kier LB (1970) Receptor mapping using mo theory. In: Danielli JF, Moran JF, Triggle DJ
(eds) Fundamental concepts in drug-receptor interactions, Academic Press: New York
51. Kier LB (ed) (1971) MO theory in drug research. Academic Press, New York, pp 164–169
52. Evans BE, Rittle KE, Bock MG et al (1988) Methods for drug discovery: development of
potent, selective, orally effective cholecystokinin antagonists. J Med Chem 31:2235–2246
53. Thompson LA, Ellman JA (1966) Synthesis and applications of small molecule libraries.
Chem Rev 96:555–600
54. Wermuth CG (1998) Search for new lead compounds: the example of the chemical and
pharmacological dissection of aminopyridazines. J Heterocycl Chem 35:1091–1100
55. Woods DD, Fildes P (1940) The anti-sulphanilamide activity (in vitro) ofp-aminobenzoic
acid and related compounds. Chem Ind 59:133–134
56. Easson LH, Stedman E (1933) Studies on the relationship between chemical constitution and
physiological action. V. Molecular dissymmetry and physiological activity. Biochem J
27:1257–1266
57. Peroutka SJ, U’Prichard DC, Greenberg DA et al (1977) Neuroleptic drug interactions with
norepinephrine alpha receptor binding sites in rat brain. Neuropharmacology 16:549–556
58. Pullmann B, Coubeils JL, Courrière P et al (1972) Quantum mechanical study of the
conformational properties of phenethylamines of biochemical and medicinal interest. J Med
Chem 15:17–23
59. Leach AR, Gillet VJ, Lewis RA (2010) Three-dimensional pharmacophore methods in drug
discovery. J Med Chem 53:539–558
60. Güner OF (2002) History and evolution of the pharmacophore concept in computer-aided
drug design. Curr Top Med Chem 2:1321–1332
61. Maynard AJ (2004) HypoGenRefine and HipHopRefine: pharmacophore refinement using
steric information from inactive compounds. Presented at the ACS national meeting, Spring,
2004
62. Jones G, Willett P, Glen R (2000) GASP: genetic algorithm superposition program. In:
Pharmacophore perception, development, and use in drug design, vol 2. International
University Line, La Jolla, CA, USA, pp 85–106
63. Jones G, Willett P, Glen RC (1995) A genetic algorithm for flexible molecular overlay and
pharmacophore elucidation. J Comput Aided Mol Des 9:532–549
64. GALAHAD. Tripos, St. Louis, MO. http://www.tripos.com/
65. Lin A, Overview of pharmacophore applications in MOE. http://www.chemcomp.com/
journal/ph4.htm
66. Vlachakis D, Fakourelis P, Makris C, Kossida S (2015) DrugOn: a fully integrated
pharmacophore modeling and structure optimization toolkit. PeerJ 3:e725
67. Khedkar SA, Malde AK, Coutinho EC et al (2007) Pharmacophore modeling in drug
discovery and development: an overview. Med Chem 3:187–197
68. Langer T, Hoffmann RD (eds) (2006) Pharmacophores and pharmacophore searches,
pharmacophores and pharmacophore searches. Wiley-VCH Verlag GmbH & Co. KGaA,
Weinheim
69. Finn PW, Kavraki LE, Latombe JC et al (1997) Rapid: randomized pharmacophore
identification for drug design. Comput Geom Theor Appl 10:263–272
70. Crandell C, Smith D (1983) Computer-assisted examination of compounds for common
three-dimensional substructures. J Chem Inf Comp Sci 23:186–197
71. Martin YC (2000) DISCO: what we did right and what we missed. In: Pharmacophore
perception, development, and use in drug design. International University Line, pp 49–68
72. Dolata D, Parrill A, Walters W (1998) CLEW: the generation of pharmacophore hypotheses
through machine learning. SAR QSAR Environ Res 9:53–81
73. Chen X, Rusinko A III, Tropsha A et al (1999) Automated pharmacophore Identification for
large chemical data sets. J Chem Inf Comput Sci 39:887–896
Pharmacophore Modelling and Screening: Concepts, Recent …
51
muscarine, and muscarone. Mol Pharmacol 3:487–494
50. Kier LB (1970) Receptor mapping using mo theory. In: Danielli JF, Moran JF, Triggle DJ
(eds) Fundamental concepts in drug-receptor interactions, Academic Press: New York
51. Kier LB (ed) (1971) MO theory in drug research. Academic Press, New York, pp 164–169
52. Evans BE, Rittle KE, Bock MG et al (1988) Methods for drug discovery: development of
potent, selective, orally effective cholecystokinin antagonists. J Med Chem 31:2235–2246
53. Thompson LA, Ellman JA (1966) Synthesis and applications of small molecule libraries.
Chem Rev 96:555–600
54. Wermuth CG (1998) Search for new lead compounds: the example of the chemical and
pharmacological dissection of aminopyridazines. J Heterocycl Chem 35:1091–1100
55. Woods DD, Fildes P (1940) The anti-sulphanilamide activity (in vitro) ofp-aminobenzoic
acid and related compounds. Chem Ind 59:133–134
56. Easson LH, Stedman E (1933) Studies on the relationship between chemical constitution and
physiological action. V. Molecular dissymmetry and physiological activity. Biochem J
27:1257–1266
57. Peroutka SJ, U’Prichard DC, Greenberg DA et al (1977) Neuroleptic drug interactions with
norepinephrine alpha receptor binding sites in rat brain. Neuropharmacology 16:549–556
58. Pullmann B, Coubeils JL, Courrière P et al (1972) Quantum mechanical study of the
conformational properties of phenethylamines of biochemical and medicinal interest. J Med
Chem 15:17–23
59. Leach AR, Gillet VJ, Lewis RA (2010) Three-dimensional pharmacophore methods in drug
discovery. J Med Chem 53:539–558
60. Güner OF (2002) History and evolution of the pharmacophore concept in computer-aided
drug design. Curr Top Med Chem 2:1321–1332
61. Maynard AJ (2004) HypoGenRefine and HipHopRefine: pharmacophore refinement using
steric information from inactive compounds. Presented at the ACS national meeting, Spring,
2004
62. Jones G, Willett P, Glen R (2000) GASP: genetic algorithm superposition program. In:
Pharmacophore perception, development, and use in drug design, vol 2. International
University Line, La Jolla, CA, USA, pp 85–106
63. Jones G, Willett P, Glen RC (1995) A genetic algorithm for flexible molecular overlay and
pharmacophore elucidation. J Comput Aided Mol Des 9:532–549
64. GALAHAD. Tripos, St. Louis, MO. http://www.tripos.com/
65. Lin A, Overview of pharmacophore applications in MOE. http://www.chemcomp.com/
journal/ph4.htm
66. Vlachakis D, Fakourelis P, Makris C, Kossida S (2015) DrugOn: a fully integrated
pharmacophore modeling and structure optimization toolkit. PeerJ 3:e725
67. Khedkar SA, Malde AK, Coutinho EC et al (2007) Pharmacophore modeling in drug
discovery and development: an overview. Med Chem 3:187–197
68. Langer T, Hoffmann RD (eds) (2006) Pharmacophores and pharmacophore searches,
pharmacophores and pharmacophore searches. Wiley-VCH Verlag GmbH & Co. KGaA,
Weinheim
69. Finn PW, Kavraki LE, Latombe JC et al (1997) Rapid: randomized pharmacophore
identification for drug design. Comput Geom Theor Appl 10:263–272
70. Crandell C, Smith D (1983) Computer-assisted examination of compounds for common
three-dimensional substructures. J Chem Inf Comp Sci 23:186–197
71. Martin YC (2000) DISCO: what we did right and what we missed. In: Pharmacophore
perception, development, and use in drug design. International University Line, pp 49–68
72. Dolata D, Parrill A, Walters W (1998) CLEW: the generation of pharmacophore hypotheses
through machine learning. SAR QSAR Environ Res 9:53–81
73. Chen X, Rusinko A III, Tropsha A et al (1999) Automated pharmacophore Identification for
large chemical data sets. J Chem Inf Comput Sci 39:887–896
Pharmacophore Modelling and Screening: Concepts, Recent …
51