J Comput Chem 22:501–508. https://doi.org/10.1002/1096-987x(20010415)22:5%3c501:
aid-jcc1021%3e3.0.co;2-v
238. Salomon-Ferrer R, Case DA, Walker RC (2013) An overview of the amber biomolecular
simulation package. Wiley Interdiscip Rev Comput Mol Sci 3:198–210. https://doi.org/10.
1002/wcms.1121
239. Miller BR, McGee TD, Swails JM et al (2012) MMPBSA.py: an efficient program for
end-state free energy calculations. J Chem Theory Comput 8:3314–3321. https://doi.org/10.
1021/ct300418h
240. Marlow MS, Dogan J, Frederick KK et al (2010) The role of conformational entropy in
molecular recognition by calmodulin. Nat Chem Biol 6:352–358. https://doi.org/10.1038/
nchembio.347
241. Kasinath V, Sharp KA, Wand AJ (2013) Microscopic insights into the NMR
relaxation-based protein conformational entropy meter. J Am Chem Soc 135:15092–
15100. https://doi.org/10.1021/ja405200u
242. Diehl C, Engström O, Delaine T et al (2010) Protein flexibility and conformational entropy
in ligand design targeting the carbohydrate recognition domain of galectin-3. J Am Chem
Soc 132:14577–14589. https://doi.org/10.1021/ja105852y
243. Fenley AT, Muddana HS, Gilson MK (2012) Entropy-enthalpy transduction caused by
conformational shifts can obscure the forces driving protein-ligand binding. Proc Natl Acad
Sci U S A 109:20006–20011. https://doi.org/10.1073/pnas.1213180109
244. Chodera JD, Mobley DL (2013) Entropy-enthalpy compensation: role and ramifications in
biomolecular ligand recognition and design. Annu Rev Biophys 42:121–142. https://doi.org/
10.1146/annurev-biophys-083012-130318
245. Olsson TSG, Ladbury JE, Pitt WR, Williams MA (2011) Extent of enthalpy-entropy
compensation in protein-ligand interactions. Protein Sci 20:1607–1618. https://doi.org/10.
1002/pro.692
246. López-Blanco JR, Miyashita O, Tama F, Chacón P (2014) Normal mode analysis techniques
in structural biology. In: John Wiley & Sons Ltd (ed) eLS. John Wiley & Sons, Ltd,
Chichester, UK, p 9
247. Numata J, Wan M, Knapp E-W (2007) Conformational entropy of biomolecules: beyond the
quasi-harmonic approximation. Genome Inform 18:192–205
248. Killian BJ, Yundenfreund Kravitz J, Gilson MK (2007) Extraction of configurational
entropy from molecular simulations via an expansion approximation. J Chem Phys
127:024107. https://doi.org/10.1063/1.2746329
249. Numata J, Knapp E-W (2012) Balanced and bias-corrected computation of conformational
entropy differences for molecular trajectories. J Chem Theory Comput 8:1235–1245. https://
doi.org/10.1021/ct200910z
250. Suárez E, Díaz N, Méndez J, Suárez D (2013) CENCALC: a computational tool for
conformational entropy calculations from molecular simulations. J Comput Chem 34:2041–
2054. https://doi.org/10.1002/jcc.23350
251. Killian BJ, Kravitz JY, Somani S et al (2009) Configurational entropy in protein-peptide
binding: computational study of Tsg101 ubiquitin E2 variant domain with an HIV-derived
PTAP nonapeptide. J Mol Biol 389:315–335. https://doi.org/10.1016/j.jmb.2009.04.003
252. Fenley AT, Killian BJ, Hnizdo V et al (2014) Correlation as a determinant of configurational
entropy in supramolecular and protein systems. J Phys Chem B 118:6447–6455. https://doi.
org/10.1021/jp411588b
253. Fogolari F, Brigo a, Molinari H (2002) The Poisson-Boltzmann equation for biomolecular
electrostatics: a tool for structural biology. J Mol Recognit 15:377–392. https://doi.org/10.
1002/jmr.577
254. King BM, Silver NW, Tidor B (2012) Efficient calculation of molecular configurational
entropies using an information theoretic approximation. J Phys Chem B 116:2891–2904.
https://doi.org/10.1021/jp2068123
255. Tembre BL, Mc Cammon JA (1984) Ligand-receptor interactions. Comput Chem 8:281–
283. https://doi.org/10.1016/0097-8485(84)85020-2
In Silico Structure-Based Prediction of Receptor–Ligand Binding …
173
aid-jcc1021%3e3.0.co;2-v
238. Salomon-Ferrer R, Case DA, Walker RC (2013) An overview of the amber biomolecular
simulation package. Wiley Interdiscip Rev Comput Mol Sci 3:198–210. https://doi.org/10.
1002/wcms.1121
239. Miller BR, McGee TD, Swails JM et al (2012) MMPBSA.py: an efficient program for
end-state free energy calculations. J Chem Theory Comput 8:3314–3321. https://doi.org/10.
1021/ct300418h
240. Marlow MS, Dogan J, Frederick KK et al (2010) The role of conformational entropy in
molecular recognition by calmodulin. Nat Chem Biol 6:352–358. https://doi.org/10.1038/
nchembio.347
241. Kasinath V, Sharp KA, Wand AJ (2013) Microscopic insights into the NMR
relaxation-based protein conformational entropy meter. J Am Chem Soc 135:15092–
15100. https://doi.org/10.1021/ja405200u
242. Diehl C, Engström O, Delaine T et al (2010) Protein flexibility and conformational entropy
in ligand design targeting the carbohydrate recognition domain of galectin-3. J Am Chem
Soc 132:14577–14589. https://doi.org/10.1021/ja105852y
243. Fenley AT, Muddana HS, Gilson MK (2012) Entropy-enthalpy transduction caused by
conformational shifts can obscure the forces driving protein-ligand binding. Proc Natl Acad
Sci U S A 109:20006–20011. https://doi.org/10.1073/pnas.1213180109
244. Chodera JD, Mobley DL (2013) Entropy-enthalpy compensation: role and ramifications in
biomolecular ligand recognition and design. Annu Rev Biophys 42:121–142. https://doi.org/
10.1146/annurev-biophys-083012-130318
245. Olsson TSG, Ladbury JE, Pitt WR, Williams MA (2011) Extent of enthalpy-entropy
compensation in protein-ligand interactions. Protein Sci 20:1607–1618. https://doi.org/10.
1002/pro.692
246. López-Blanco JR, Miyashita O, Tama F, Chacón P (2014) Normal mode analysis techniques
in structural biology. In: John Wiley & Sons Ltd (ed) eLS. John Wiley & Sons, Ltd,
Chichester, UK, p 9
247. Numata J, Wan M, Knapp E-W (2007) Conformational entropy of biomolecules: beyond the
quasi-harmonic approximation. Genome Inform 18:192–205
248. Killian BJ, Yundenfreund Kravitz J, Gilson MK (2007) Extraction of configurational
entropy from molecular simulations via an expansion approximation. J Chem Phys
127:024107. https://doi.org/10.1063/1.2746329
249. Numata J, Knapp E-W (2012) Balanced and bias-corrected computation of conformational
entropy differences for molecular trajectories. J Chem Theory Comput 8:1235–1245. https://
doi.org/10.1021/ct200910z
250. Suárez E, Díaz N, Méndez J, Suárez D (2013) CENCALC: a computational tool for
conformational entropy calculations from molecular simulations. J Comput Chem 34:2041–
2054. https://doi.org/10.1002/jcc.23350
251. Killian BJ, Kravitz JY, Somani S et al (2009) Configurational entropy in protein-peptide
binding: computational study of Tsg101 ubiquitin E2 variant domain with an HIV-derived
PTAP nonapeptide. J Mol Biol 389:315–335. https://doi.org/10.1016/j.jmb.2009.04.003
252. Fenley AT, Killian BJ, Hnizdo V et al (2014) Correlation as a determinant of configurational
entropy in supramolecular and protein systems. J Phys Chem B 118:6447–6455. https://doi.
org/10.1021/jp411588b
253. Fogolari F, Brigo a, Molinari H (2002) The Poisson-Boltzmann equation for biomolecular
electrostatics: a tool for structural biology. J Mol Recognit 15:377–392. https://doi.org/10.
1002/jmr.577
254. King BM, Silver NW, Tidor B (2012) Efficient calculation of molecular configurational
entropies using an information theoretic approximation. J Phys Chem B 116:2891–2904.
https://doi.org/10.1021/jp2068123
255. Tembre BL, Mc Cammon JA (1984) Ligand-receptor interactions. Comput Chem 8:281–
283. https://doi.org/10.1016/0097-8485(84)85020-2
In Silico Structure-Based Prediction of Receptor–Ligand Binding …
173