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101. Schindler T et al (2000) Structural mechanism for STI-571 inhibition of abelson tyrosine
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102. Varghese JN (1999) Development of neuraminidase inhibitors as anti-influenza virus drugs.
Drug Dev Res 46(3–4):176–196
103. Rutenber EE, Stroud RM (1996) Binding of the anticancer drug ZD1694 to E. coli
thymidylate synthase: assessing specificity and affinity. Structure 4(11):1317–1324
104. Filikov AV et al (2000) Identification of ligands for RNA targets via structure-based virtual
screening: HIV-1 TAR. J Comput Aided Mol Des 14(6):593–610
268
S. Loharch et al.
proteins: an extensive study of ligand reorganization upon binding. J Med Chem 47(10):
2499–2510
81. Bostrom J (2001) Reproducing the conformations of protein-bound ligands: a critical
evaluation of several popular conformational searching tools. J Comput Aided Mol Des
15(12):1137–1152
82. Chen IJ, Foloppe N (2008) Conformational sampling of druglike molecules with MOE and
catalyst: implications for pharmacophore modeling and virtual screening. J Chem Inf Model
48(9):1773–1791
83. Stahura FL, Bajorath J (2005) New methodologies for ligand-based virtual screening. Curr
Pharm Des 11(9):1189–1202
84. Lorber DM, Shoichet BK (1998) Flexible ligand docking using conformational ensembles.
Protein Sci 7(4):938–950
85. Lyne PD (2002) Structure-based virtual screening: an overview. Drug Discov Today 7
(20):1047–1055
86. Sadowski J, Gasteiger J, Klebe G (1994) Comparison of automatic three-dimensional model
builders using 639 X-ray structures. J Chem Inf Comput Sci 34(4):1000–1008
87. Kirchmair J et al (2006) Comparative performance assessment of the conformational model
generators omega and catalyst: a large-scale survey on the retrieval of protein-bound ligand
conformations. J Chem Inf Model 46(4):1848–1861
88. Vainio MJ, Johnson MS (2007) Generating conformer ensembles using a multiobjective
genetic algorithm. J Chem Inf Model 47(6):2462–2474
89. Liu X et al (2009) Cyndi: a multi-objective evolution algorithm based method for bioactive
molecular conformational generation. BMC Bioinformatics 10:101
90. Blaney JM, Dixon JS (2007) Distance geometry in molecular modeling. In: Lipkowitz KB,
Boyd DB (eds) Reviews in computational chemistry. pp 299–335
91. Wild, DJ, Blankley CJ (1999) VisualiSAR: a web-based application for clustering, structure
browsing, and structure-activity relationship study. J Mol Graph Model 17(2):85–89, 120–125
92. Nicholls A et al (2010) Molecular shape and medicinal chemistry: a perspective. J Med
Chem 53(10):3862–3886
93. Bohm HJ, Flohr A, Stahl M (2004) Scaffold hopping. Drug Discov Today Technol 1(3):
217–224
94. Willett P (1987) A review of chemical structure retrieval systems. J Chemom 1(3):139–155
95. Scott DE et al (2012) Fragment-based approaches in drug discovery and chemical biology.
Biochemistry 51(25):4990–5003
96. Lewell XQ et al (1998) RECAP–retrosynthetic combinatorial analysis procedure: a powerful
new technique for identifying privileged molecular fragments with useful applications in
combinatorial chemistry. J Chem Inf Comput Sci 38(3):511–522
97. Varin T et al (2010) Compound set enrichment: a novel approach to analysis of primary HTS
data. J Chem Inf Model 50(12):2067–2078
98. Dandapani S et al (2012) Selecting, acquiring, and using small molecule libraries for
high-throughput screening. Curr Protoc Chem Biol 4:177–191
99. Petrova T et al (2012) Structural enrichment of HTS compounds from available commercial
libraries. MedChemComm 3(5):571–579
100. Kaldor SW et al (1997) Viracept (nelfinavir mesylate, AG1343): a potent, orally bioavailable
inhibitor of HIV-1 protease. J Med Chem 40(24):3979–3985
101. Schindler T et al (2000) Structural mechanism for STI-571 inhibition of abelson tyrosine
kinase. Science 289(5486):1938–1942
102. Varghese JN (1999) Development of neuraminidase inhibitors as anti-influenza virus drugs.
Drug Dev Res 46(3–4):176–196
103. Rutenber EE, Stroud RM (1996) Binding of the anticancer drug ZD1694 to E. coli
thymidylate synthase: assessing specificity and affinity. Structure 4(11):1317–1324
104. Filikov AV et al (2000) Identification of ligands for RNA targets via structure-based virtual
screening: HIV-1 TAR. J Comput Aided Mol Des 14(6):593–610
268
S. Loharch et al.