74. Handschuh S, Wagener M, Gasteiger JJ (1998) Superposition of three-dimensional chemical
structures allowing for conformational flexibility by a hybrid method. J Chem Inf Comput
Sci 38:220–232
75. Holliday J, Willet P (1997) Using a genetic algorithm to identify common structural features
in sets of ligands. J Mol Graph Model 15:203–253
76. Bron C, Kerbosch J (1973) Algorithm 457: finding all cliques of an undirected graph.
Commun ACM 16:575–577
77. Brint A, Willett P (1987) Algorithms for the identification of three-dimensional maximal
common substructures. J Chem Inf Comp Sci 27:152–158
78. Guilloux VL, Schmidtke P, Tuffery P (2009) Fpocket: an open source platform for ligand
pocket detection. BMC Bioinform 10:168–178
79. Schmidtke P, Bidon-Chanal A, Luque FJ et al (2011) MDpocket: open-source cavity
detection and characterization on molecular dynamics trajectories. Bioinformatics 27:3276–
3285
80. Carlson HA, Masukawa KM, Rubins K et al (2000) Developing a dynamic pharmacophore
model for HIV-1 integrase. J Med Chem 43:2100–2114
81. Masukawa KM, Carlson HA, McCammon JA (2000) Technique for developing a
pharmacophore model that accommodates inherent protein flexibility: an application to
HIV-1 integrase. In: Guner OF (ed) Pharmacophore perception, development, and use in
drug design. International University Line
82. Clark DE, Westhead DR, Sykes RA et al (1996) Active-site-directed 3D database searching:
pharmacophore extraction and validation of hits. J Comput Aided Mol Des 10:397–416
83. Mahadevi AS, Sastry GN (2013) Cation-p interaction: its role and relevance in chemistry,
biology and material science. Chem Rev 113:2100–2138
84. Chourasia M, Sastry GM, Sastry GN (2011) Aromatic—aromatic database, A2ID: an
analysis of aromatic networks in proteins. Int J Biol Macromol 48:540–552
85. Saha S, Sastry GN (2015) Cooperative or anticooperative: how noncovalent interactions
influence each other. J Phys Chem B 119:11121–11135
86. Badrinarayan P, Choudhury C, Sastry GN (2015) Molecular modeling. In: Dhar PK and
Singh V (eds) Systems and synthetic biology (S2B2). Springer Press, pp 93–128
87. Wolber G, Langer T (2005) LigandScout: 3-D pharmacophores derived from protein-bound
ligands and their use as virtual screening filters. J Chem Inf Model 45:160–169
88. Salam NK, Nuti R, Sherman W (2009) Novel method for generating structure-based
pharmacophores using energetic analysis. J Chem Inf Model 49:2356–2368
89. Friesner R, Murphy RB, Repasky MP et al (2006) Extra precision glide: docking and scoring
incorporating a model of hydrophobic enclosure for protein-ligand complexes. J Med Chem
49:6177–6196
90. Carlson HA, Masukawa KM, McCammon JA (1999) Method for including the dynamic
fluctuations of a protein in computer-aided drug design. J Phys Chem A 103:10213–10219
91. McGregor MJ, Muskal SM (1999) Pharmacophore fingerprinting. 1. Application to QSAR
and focused library design. J Chem Inf Comput Sci 39:569–574
92. McGregor MJ, Muskal SM (2000) Pharmacophore fingerprinting. 2. Application to primary
library design. J Chem Inf Comput Sci 40:117–125
93. Voet AR, Kumar A, Berenger F et al (2014) Combining in silico and in cerebro approaches
for virtual screening and pose prediction in SAMPL4. J Comput Aided Mol Des 28:363–373
94. Voet A, Helsen C, Zhang KY et al (2013) The discovery of novel human androgen receptor
antagonist chemotypes using a combined pharmacophore screening procedure. Chem Med
Chem 8:644–651
95. Loving K, Salam NK, Sherman W (2009) Energetic analysis of fragment docking and
application to structure-based pharmacophore hypothesis generation. J Comput Aided Mol
Des 23:541–554
96. Anuradha A, Trivelli X, Guérardel Y et al (2007) Thiacetazone, an antitubercular drug that
inhibits cyclopropanation of cell wall mycolic acids in mycobacteria. PLoS ONE 12:e1343
52
C. Choudhury and G. Narahari Sastry
structures allowing for conformational flexibility by a hybrid method. J Chem Inf Comput
Sci 38:220–232
75. Holliday J, Willet P (1997) Using a genetic algorithm to identify common structural features
in sets of ligands. J Mol Graph Model 15:203–253
76. Bron C, Kerbosch J (1973) Algorithm 457: finding all cliques of an undirected graph.
Commun ACM 16:575–577
77. Brint A, Willett P (1987) Algorithms for the identification of three-dimensional maximal
common substructures. J Chem Inf Comp Sci 27:152–158
78. Guilloux VL, Schmidtke P, Tuffery P (2009) Fpocket: an open source platform for ligand
pocket detection. BMC Bioinform 10:168–178
79. Schmidtke P, Bidon-Chanal A, Luque FJ et al (2011) MDpocket: open-source cavity
detection and characterization on molecular dynamics trajectories. Bioinformatics 27:3276–
3285
80. Carlson HA, Masukawa KM, Rubins K et al (2000) Developing a dynamic pharmacophore
model for HIV-1 integrase. J Med Chem 43:2100–2114
81. Masukawa KM, Carlson HA, McCammon JA (2000) Technique for developing a
pharmacophore model that accommodates inherent protein flexibility: an application to
HIV-1 integrase. In: Guner OF (ed) Pharmacophore perception, development, and use in
drug design. International University Line
82. Clark DE, Westhead DR, Sykes RA et al (1996) Active-site-directed 3D database searching:
pharmacophore extraction and validation of hits. J Comput Aided Mol Des 10:397–416
83. Mahadevi AS, Sastry GN (2013) Cation-p interaction: its role and relevance in chemistry,
biology and material science. Chem Rev 113:2100–2138
84. Chourasia M, Sastry GM, Sastry GN (2011) Aromatic—aromatic database, A2ID: an
analysis of aromatic networks in proteins. Int J Biol Macromol 48:540–552
85. Saha S, Sastry GN (2015) Cooperative or anticooperative: how noncovalent interactions
influence each other. J Phys Chem B 119:11121–11135
86. Badrinarayan P, Choudhury C, Sastry GN (2015) Molecular modeling. In: Dhar PK and
Singh V (eds) Systems and synthetic biology (S2B2). Springer Press, pp 93–128
87. Wolber G, Langer T (2005) LigandScout: 3-D pharmacophores derived from protein-bound
ligands and their use as virtual screening filters. J Chem Inf Model 45:160–169
88. Salam NK, Nuti R, Sherman W (2009) Novel method for generating structure-based
pharmacophores using energetic analysis. J Chem Inf Model 49:2356–2368
89. Friesner R, Murphy RB, Repasky MP et al (2006) Extra precision glide: docking and scoring
incorporating a model of hydrophobic enclosure for protein-ligand complexes. J Med Chem
49:6177–6196
90. Carlson HA, Masukawa KM, McCammon JA (1999) Method for including the dynamic
fluctuations of a protein in computer-aided drug design. J Phys Chem A 103:10213–10219
91. McGregor MJ, Muskal SM (1999) Pharmacophore fingerprinting. 1. Application to QSAR
and focused library design. J Chem Inf Comput Sci 39:569–574
92. McGregor MJ, Muskal SM (2000) Pharmacophore fingerprinting. 2. Application to primary
library design. J Chem Inf Comput Sci 40:117–125
93. Voet AR, Kumar A, Berenger F et al (2014) Combining in silico and in cerebro approaches
for virtual screening and pose prediction in SAMPL4. J Comput Aided Mol Des 28:363–373
94. Voet A, Helsen C, Zhang KY et al (2013) The discovery of novel human androgen receptor
antagonist chemotypes using a combined pharmacophore screening procedure. Chem Med
Chem 8:644–651
95. Loving K, Salam NK, Sherman W (2009) Energetic analysis of fragment docking and
application to structure-based pharmacophore hypothesis generation. J Comput Aided Mol
Des 23:541–554
96. Anuradha A, Trivelli X, Guérardel Y et al (2007) Thiacetazone, an antitubercular drug that
inhibits cyclopropanation of cell wall mycolic acids in mycobacteria. PLoS ONE 12:e1343
52
C. Choudhury and G. Narahari Sastry