219. O’Boyle N, Vandermeersch T, Hutchison G (2011) Confab—generation of diverse low
energy conformers. J Cheminform 3:P32. https://doi.org/10.1186/1758-2946-3-s1-p32
220. Gasteiger J, Rudolph C, Sadowski J (1990) Automatic generation of 3D-atomic coordinates
for organic molecules. Tetrahedron Comput Methodol 3:537–547. https://doi.org/10.1016/
0898-5529(90)90156-3
221. Riniker S, Landrum GA (2015) Better informed distance geometry: using what we know to
improve conformation generation. J Chem Inf Model 55:2562–2574. https://doi.org/10.
1021/acs.jcim.5b00654
222. Miteva MA, Guyon F, Tuffery P (2010) Frog2: efficient 3D conformation ensemble
generator for small compounds. Nucl Acids Res 38:W622–W627. https://doi.org/10.1093/
nar/gkq325
223. Sauton N, Lagorce D, Villoutreix BO, Miteva MA (2008) MS-DOCK: accurate multiple
conformation generator and rigid docking protocol for multi-step virtual ligand screening.
BMC Bioinform 9:1–12. https://doi.org/10.1186/1471-2105-9-184
224. Greg L (2018) RDKit: open-source cheminformatics. http://www.rdkit.org/. Accessed 7 Feb
2018
225. Sabbadin D, Moro S (2014) Supervised molecular dynamics (SuMD) as a helpful tool to
depict GPCR-ligand recognition pathway in a nanosecond time scale. J Chem Inf Model
54:372–376. https://doi.org/10.1021/ci400766b
226. Mobley DL, Gilson MK (2017) Predicting binding free energies: frontiers and benchmarks.
Annu Rev Biophys 46:531–558. https://doi.org/10.1146/annurev-biophys-070816-033654
227. Chodera JD, Mobley DL, Shirts MR et al (2011) Alchemical free energy methods for drug
discovery: progress and challenges. Curr Opin Struct Biol 21:150–160. https://doi.org/10.
1016/j.sbi.2011.01.011
228. Shirts MR, Mobley DL, Brown SP (2010) Free-energy calculations in structure-based drug
design. In: Merz KM, Ringe D, Reynolds CH (eds) Drug design: structure-and ligand-based
approaches. Cambridge University Press, New York, Cambridge, pp 61–86
229. Hansen N, Van Gunsteren WF (2014) Practical aspects of free-energy calculations: a review.
J Chem Theory Comput 10:2632–2647. https://doi.org/10.1021/ct500161f
230. Christ CD, Mark AE, van Gunsteren WF (2009) Basic ingredients of free energy
calculations: a review. J Comput Chem 31:1569-1582. https://doi.org/10.1002/jcc.21450
231. Genheden S, Ryde U (2015) The MM/PBSA and MM/GBSA methods to estimate
ligand-binding affinities. Expert Opin Drug Discov 10:449–461. https://doi.org/10.1517/
17460441.2015.1032936
232. Homeyer N, Gohlke H (2012) Free energy calculations by the molecular mechanics
Poisson-Boltzmann surface area method. Mol Inform 31:114–122. https://doi.org/10.1002/
minf.201100135
233. Case DA, Babin V, Berryman JT, Betz RM, Cai Q, Cerutti DS, Cheatham TE III,
Darden TA, Duke RE, Gohlke H, Goetz AW, Gusarov S, Homeyer N, Janowski P, Kaus J,
Kolossváry I, Kovalenko A, Lee TS, LeGrand S, Luchko T, Luo R, Madej B, Merz KM,
Paesani F, Roe DR, Roitberg A, Sagui C, Salomon-Ferrer R, Seabra G, Simmerling CL,
Smith W, Swails J, Walker RC, Wang J, Wolf RM, Wolf X, Kollman PA (2014) Amber14
Reference manual
234. Sprenger KG, Jaeger VW, Pfaendtner J (2015) The general AMBER force field (GAFF) can
accurately predict thermodynamic and transport properties of many ionic liquids. J Phys
Chem B 119:5882–5895. https://doi.org/10.1021/acs.jpcb.5b00689
235. Maier JA, Martinez C, Kasavajhala K et al (2015) ff14SB: improving the accuracy of protein
side chain and backbone parameters from ff99SB. J Chem Theory Comput 11:3696–3713.
https://doi.org/10.1021/acs.jctc.5b00255
236. Nguyen CN, Kurtzman Young T, Gilson MK (2012) Grid inhomogeneous solvation theory:
hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril. J Chem
Phys 137:044101. https://doi.org/10.1063/1.4733951
237. Kräutler V, Van Gunsteren WF, Hünenberger PH (2001) A fast SHAKE algorithm to solve
distance constraint equations for small molecules in molecular dynamics simulations.
172
S. K. Panday and I. Ghosh
energy conformers. J Cheminform 3:P32. https://doi.org/10.1186/1758-2946-3-s1-p32
220. Gasteiger J, Rudolph C, Sadowski J (1990) Automatic generation of 3D-atomic coordinates
for organic molecules. Tetrahedron Comput Methodol 3:537–547. https://doi.org/10.1016/
0898-5529(90)90156-3
221. Riniker S, Landrum GA (2015) Better informed distance geometry: using what we know to
improve conformation generation. J Chem Inf Model 55:2562–2574. https://doi.org/10.
1021/acs.jcim.5b00654
222. Miteva MA, Guyon F, Tuffery P (2010) Frog2: efficient 3D conformation ensemble
generator for small compounds. Nucl Acids Res 38:W622–W627. https://doi.org/10.1093/
nar/gkq325
223. Sauton N, Lagorce D, Villoutreix BO, Miteva MA (2008) MS-DOCK: accurate multiple
conformation generator and rigid docking protocol for multi-step virtual ligand screening.
BMC Bioinform 9:1–12. https://doi.org/10.1186/1471-2105-9-184
224. Greg L (2018) RDKit: open-source cheminformatics. http://www.rdkit.org/. Accessed 7 Feb
2018
225. Sabbadin D, Moro S (2014) Supervised molecular dynamics (SuMD) as a helpful tool to
depict GPCR-ligand recognition pathway in a nanosecond time scale. J Chem Inf Model
54:372–376. https://doi.org/10.1021/ci400766b
226. Mobley DL, Gilson MK (2017) Predicting binding free energies: frontiers and benchmarks.
Annu Rev Biophys 46:531–558. https://doi.org/10.1146/annurev-biophys-070816-033654
227. Chodera JD, Mobley DL, Shirts MR et al (2011) Alchemical free energy methods for drug
discovery: progress and challenges. Curr Opin Struct Biol 21:150–160. https://doi.org/10.
1016/j.sbi.2011.01.011
228. Shirts MR, Mobley DL, Brown SP (2010) Free-energy calculations in structure-based drug
design. In: Merz KM, Ringe D, Reynolds CH (eds) Drug design: structure-and ligand-based
approaches. Cambridge University Press, New York, Cambridge, pp 61–86
229. Hansen N, Van Gunsteren WF (2014) Practical aspects of free-energy calculations: a review.
J Chem Theory Comput 10:2632–2647. https://doi.org/10.1021/ct500161f
230. Christ CD, Mark AE, van Gunsteren WF (2009) Basic ingredients of free energy
calculations: a review. J Comput Chem 31:1569-1582. https://doi.org/10.1002/jcc.21450
231. Genheden S, Ryde U (2015) The MM/PBSA and MM/GBSA methods to estimate
ligand-binding affinities. Expert Opin Drug Discov 10:449–461. https://doi.org/10.1517/
17460441.2015.1032936
232. Homeyer N, Gohlke H (2012) Free energy calculations by the molecular mechanics
Poisson-Boltzmann surface area method. Mol Inform 31:114–122. https://doi.org/10.1002/
minf.201100135
233. Case DA, Babin V, Berryman JT, Betz RM, Cai Q, Cerutti DS, Cheatham TE III,
Darden TA, Duke RE, Gohlke H, Goetz AW, Gusarov S, Homeyer N, Janowski P, Kaus J,
Kolossváry I, Kovalenko A, Lee TS, LeGrand S, Luchko T, Luo R, Madej B, Merz KM,
Paesani F, Roe DR, Roitberg A, Sagui C, Salomon-Ferrer R, Seabra G, Simmerling CL,
Smith W, Swails J, Walker RC, Wang J, Wolf RM, Wolf X, Kollman PA (2014) Amber14
Reference manual
234. Sprenger KG, Jaeger VW, Pfaendtner J (2015) The general AMBER force field (GAFF) can
accurately predict thermodynamic and transport properties of many ionic liquids. J Phys
Chem B 119:5882–5895. https://doi.org/10.1021/acs.jpcb.5b00689
235. Maier JA, Martinez C, Kasavajhala K et al (2015) ff14SB: improving the accuracy of protein
side chain and backbone parameters from ff99SB. J Chem Theory Comput 11:3696–3713.
https://doi.org/10.1021/acs.jctc.5b00255
236. Nguyen CN, Kurtzman Young T, Gilson MK (2012) Grid inhomogeneous solvation theory:
hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril. J Chem
Phys 137:044101. https://doi.org/10.1063/1.4733951
237. Kräutler V, Van Gunsteren WF, Hünenberger PH (2001) A fast SHAKE algorithm to solve
distance constraint equations for small molecules in molecular dynamics simulations.
172
S. K. Panday and I. Ghosh