162. Cheng F, Li W, Wu Z, Wang X, Zhang C, Li J, Liu G, Tang Y (2013). Prediction of
polypharmacological profiles of drugs by the integration of chemical, side effect, and
therapeutic space. J Chem Inf Model 53(4):753–762
163. Bender A, Scheiber J, Glick M, Davies JW, Azzaoui K, Hamon J, Urban L, Whitebread S,
Jenkins JL (2007) Analysis of pharmacology data and the prediction of adverse drug
reactions and off-target effects from chemical structure. ChemMedChem 2(6):861–873
164. Unterthiner T, Mayr A, Klambauer G, Steijaert M, Wegner JK, Ceulemans H, Hochreiter S
(2014) Deep learning as an opportunity in virtual screening. In: Proceedings of the deep
learning workshop at NIPS
165. Mestres J, Martín-Couce L, Gregori-Puigjané E, Cases M, Boyer S (2006) Ligand-based
approach to in silico pharmacology: nuclear receptor profiling. J Chem Inf Model 46
(6):2725–2736
166. Gregori-Puigjané E, Mestres J (2008) A ligand-based approach to mining the chemogenomic
space of drugs. Comb Chem High Throughput Screening 11(8):669–676
167. Willett P, Barnard JM, Downs GM (1998) Chemical similarity searching. J Chem Inf
Comput Sci 38(6):983–996
168. Zhou B, Wang R, Wu P, Kong DX (2015) Drug repurposing based on drug-drug interaction.
Chem Biol Drug Des 85(2):137–144
169. Gane PJ, Dean PM (2000) Recent advances in structure-based rational drug design. Curr
Opin Struct Biol 10(4):401–404
170. Alvarez JC (2004) High-throughput docking as a source of novel drug leads. Curr Opin
Chem Biol 8(4):365–370
171. Rarey M, Kramer B, Lengauer T (1999) The particle concept: placing discrete water
molecules during protein-ligand docking predictions. Proteins: Struct Funct Bioinf 34(1):17–
28
172. Corbeil CR, Englebienne P, Moitessier N (2007) Docking ligands into flexible and solvated
macromolecules. 1. Development and validation of FITTED 1.0. J Chem Inf Model 47
(2):435–449
173. Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) Development and validation of a
genetic algorithm for flexible docking. J Mol Biol 267(3):727–748
174. Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP,
Knoll EH, Shelley M, Perry JK, Shaw DE, Francis P, Shenkin PS (2004) Glide: a new
approach for rapid, accurate docking and scoring. 1. Method and assessment of docking
accuracy. J Med Chem 47(7):1739–1749
175. Jain AN (2003) Surflex: fully automatic flexible molecular docking using a molecular
similarity-based search engine. J Med Chem 46(4):499–511
176. Velec HF, Gohlke H, Klebe G (2005) DrugScoreCSD knowledge-based scoring function
derived from small molecule crystal data with superior recognition rate of near-native ligand
poses and better affinity prediction. J Med Chem 48(20):6296–6303
177. Meng EC, Shoichet BK, Kuntz ID (1992) Automated docking with grid-based energy
evaluation. J Comput Chem 13(4):505–524
178. Abagyan R, Totrov M, Kuznetsov D (1994) ICM—a new method for protein modeling and
design: applications to docking and structure prediction from the distorted native
conformation. J Comput Chem 15(5):488–506
179. McMartin C, Bohacek RS (1997) QXP: powerful, rapid computer algorithms for
structure-based drug design. J Comput Aided Mol Des 11(4):333–344
180. Moitessier N, Englebienne P, Lee D, Lawandi J, Corbeil AC (2008) Towards the
development of universal, fast and highly accurate docking/scoring methods: a long way to
go. Br J Pharm 153(S1)
181. Brooijmans N, Kuntz ID (2003) Molecular recognition and docking algorithms. Annu Rev
Biophys Biomol Struct 32(1):335–373
182. Mysinger MM, Shoichet BK (2010) Rapid context-dependent ligand desolvation in
molecular docking. J Chem Inf Model 50(9):1561–1573
183. Schrödinger L (2009) Schrödinger Suite 2009. LLC, New York, NY
Structure-Based Drug Design…
303
polypharmacological profiles of drugs by the integration of chemical, side effect, and
therapeutic space. J Chem Inf Model 53(4):753–762
163. Bender A, Scheiber J, Glick M, Davies JW, Azzaoui K, Hamon J, Urban L, Whitebread S,
Jenkins JL (2007) Analysis of pharmacology data and the prediction of adverse drug
reactions and off-target effects from chemical structure. ChemMedChem 2(6):861–873
164. Unterthiner T, Mayr A, Klambauer G, Steijaert M, Wegner JK, Ceulemans H, Hochreiter S
(2014) Deep learning as an opportunity in virtual screening. In: Proceedings of the deep
learning workshop at NIPS
165. Mestres J, Martín-Couce L, Gregori-Puigjané E, Cases M, Boyer S (2006) Ligand-based
approach to in silico pharmacology: nuclear receptor profiling. J Chem Inf Model 46
(6):2725–2736
166. Gregori-Puigjané E, Mestres J (2008) A ligand-based approach to mining the chemogenomic
space of drugs. Comb Chem High Throughput Screening 11(8):669–676
167. Willett P, Barnard JM, Downs GM (1998) Chemical similarity searching. J Chem Inf
Comput Sci 38(6):983–996
168. Zhou B, Wang R, Wu P, Kong DX (2015) Drug repurposing based on drug-drug interaction.
Chem Biol Drug Des 85(2):137–144
169. Gane PJ, Dean PM (2000) Recent advances in structure-based rational drug design. Curr
Opin Struct Biol 10(4):401–404
170. Alvarez JC (2004) High-throughput docking as a source of novel drug leads. Curr Opin
Chem Biol 8(4):365–370
171. Rarey M, Kramer B, Lengauer T (1999) The particle concept: placing discrete water
molecules during protein-ligand docking predictions. Proteins: Struct Funct Bioinf 34(1):17–
28
172. Corbeil CR, Englebienne P, Moitessier N (2007) Docking ligands into flexible and solvated
macromolecules. 1. Development and validation of FITTED 1.0. J Chem Inf Model 47
(2):435–449
173. Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) Development and validation of a
genetic algorithm for flexible docking. J Mol Biol 267(3):727–748
174. Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP,
Knoll EH, Shelley M, Perry JK, Shaw DE, Francis P, Shenkin PS (2004) Glide: a new
approach for rapid, accurate docking and scoring. 1. Method and assessment of docking
accuracy. J Med Chem 47(7):1739–1749
175. Jain AN (2003) Surflex: fully automatic flexible molecular docking using a molecular
similarity-based search engine. J Med Chem 46(4):499–511
176. Velec HF, Gohlke H, Klebe G (2005) DrugScoreCSD knowledge-based scoring function
derived from small molecule crystal data with superior recognition rate of near-native ligand
poses and better affinity prediction. J Med Chem 48(20):6296–6303
177. Meng EC, Shoichet BK, Kuntz ID (1992) Automated docking with grid-based energy
evaluation. J Comput Chem 13(4):505–524
178. Abagyan R, Totrov M, Kuznetsov D (1994) ICM—a new method for protein modeling and
design: applications to docking and structure prediction from the distorted native
conformation. J Comput Chem 15(5):488–506
179. McMartin C, Bohacek RS (1997) QXP: powerful, rapid computer algorithms for
structure-based drug design. J Comput Aided Mol Des 11(4):333–344
180. Moitessier N, Englebienne P, Lee D, Lawandi J, Corbeil AC (2008) Towards the
development of universal, fast and highly accurate docking/scoring methods: a long way to
go. Br J Pharm 153(S1)
181. Brooijmans N, Kuntz ID (2003) Molecular recognition and docking algorithms. Annu Rev
Biophys Biomol Struct 32(1):335–373
182. Mysinger MM, Shoichet BK (2010) Rapid context-dependent ligand desolvation in
molecular docking. J Chem Inf Model 50(9):1561–1573
183. Schrödinger L (2009) Schrödinger Suite 2009. LLC, New York, NY
Structure-Based Drug Design…
303