52. Ben-Shalom IY, Pfeiffer-Marek S, Baringhaus
KH et al (2017) Efficient approximation of
ligand rotational and translational entropy
changes upon binding for use in MM-PBSA
calculations. J Chem Inf Model 57:170–189
53. Hou T, Guo S, Xu X (2002) Predictions of
binding of a diverse set of ligands to
gelatinase-A by a combination of molecular
dynamics and continuum solvent models. J
Phys Chem B 106:5527–5535
54. Gouda H, Kuntz ID, Case DA et al (2003)
Free energy calculations for theophylline binding to an RNA aptamer: comparison of
MM-PBSA and thermodynamic integration
methods. Biopolymers 68:16–34
55. Hu G, Ma A, Wang J (2017) Ligand selectivity
mechanism and conformational changes in
guanine Riboswitch by molecular dynamics
simulations and free energy calculations. J
Chem Inf Model 57:918–928
56. Hou T, Chen K, McLaughlin WA et al (2006)
Computational analysis and prediction of the
binding motif and protein interacting partners
of the Abl SH3 domain. PLoS Comput Biol 2:
e1–e1
57. Stoica I, Sadiq SK, Coveney PV (2008) Rapid
and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases. J
Am Chem Soc 130:2639–2648
58. Venken T, Krnavek D, Mu ¨nch J et al (2011) An
optimized MM/PBSA virtual screening
approach applied to an HIV-1 gp41 fusion
peptide inhibitor. Proteins 79:3221–3235
59. Spiliotopoulos D, Spitaleri A, Musco G (2012)
Exploring PHD fingers and H3K4me0 interactions with molecular dynamics simulations
and binding free energy calculations: AIREPHD1, a comparative study. PLoS One 7:
e46902
60. Opuu V, Sun YJ, Hou T et al (2020) A physicsbased energy function allows the computational redesign of a PDZ domain. Sci Rep
10:11150
61. Simonson T (2003) Electrostatics and dynamics of proteins. Rep Prog Phys 66:737–737
Computational Design of Binding
255
KH et al (2017) Efficient approximation of
ligand rotational and translational entropy
changes upon binding for use in MM-PBSA
calculations. J Chem Inf Model 57:170–189
53. Hou T, Guo S, Xu X (2002) Predictions of
binding of a diverse set of ligands to
gelatinase-A by a combination of molecular
dynamics and continuum solvent models. J
Phys Chem B 106:5527–5535
54. Gouda H, Kuntz ID, Case DA et al (2003)
Free energy calculations for theophylline binding to an RNA aptamer: comparison of
MM-PBSA and thermodynamic integration
methods. Biopolymers 68:16–34
55. Hu G, Ma A, Wang J (2017) Ligand selectivity
mechanism and conformational changes in
guanine Riboswitch by molecular dynamics
simulations and free energy calculations. J
Chem Inf Model 57:918–928
56. Hou T, Chen K, McLaughlin WA et al (2006)
Computational analysis and prediction of the
binding motif and protein interacting partners
of the Abl SH3 domain. PLoS Comput Biol 2:
e1–e1
57. Stoica I, Sadiq SK, Coveney PV (2008) Rapid
and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases. J
Am Chem Soc 130:2639–2648
58. Venken T, Krnavek D, Mu ¨nch J et al (2011) An
optimized MM/PBSA virtual screening
approach applied to an HIV-1 gp41 fusion
peptide inhibitor. Proteins 79:3221–3235
59. Spiliotopoulos D, Spitaleri A, Musco G (2012)
Exploring PHD fingers and H3K4me0 interactions with molecular dynamics simulations
and binding free energy calculations: AIREPHD1, a comparative study. PLoS One 7:
e46902
60. Opuu V, Sun YJ, Hou T et al (2020) A physicsbased energy function allows the computational redesign of a PDZ domain. Sci Rep
10:11150
61. Simonson T (2003) Electrostatics and dynamics of proteins. Rep Prog Phys 66:737–737
Computational Design of Binding
255