Bibliography

[Hummer-2001]

Hummer, G.

Fast-growth thermodynamic integration: Error and efficiency analysis.

J. Chem. Phys. 2001, 114, 7330–7337

DOI: 10.1063/1.1363668

[Hummer-2002]

Hummer, G.

Fast-growth Thermodynamic Integration∶ Results for Sodium Ion Hydration.

Molecular Simulation. 2002, 28 (1-2), 81-90.

DOI: 10.1080/08927020211972

[Gapsys-2020]

Gapsys, V.; Pérez-Benito, L.; Aldeghi, M.; Seeliger, D.; van Vlijmen, H.; Tresadern, G.; de Groot, B.L.

Large Scale Relative Protein Ligand Binding Affinities Using Nonequilibrium Alchemy.

Chem. Sci. 2020, 11 (4), 1140–1152.

DOI: 10.1039/c9sc03754c

[Haider-2018]

Haider, K.; Cruz, A.; Ramsey, S.; Gilson, M.K.; Kurtzman, T.

Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories

J. Chem. Theory Comput. 2018, 14 (1), 418–425.

DOI: 10.1021/acs.jctc.7b00592

[Jarzynski-1997a]

Jarzynski, C.

Nonequilibrium Equality for Free Energy Differences.

Phys. Rev. Lett. 1997, 78 (14), 2690–2693.

DOI: 10.1103/PhysRevLett.78.2690

[Jarzynski-1997b]

Jarzynski, C.

Equilibrium Free-Energy Differences from Nonequilibrium Measurements: A Master-Equation Approach.

Phys. Rev. E 1997, 56 (5), 5018–5035.

DOI: 10.1103/physreve.56.5018

[Liu-2013]

Liu, S.; Wu, Y.; Lin, T.; Abel, R.; Redmann, J.P.; Summa, C.M.; Jaber, V.R.; Lim, N.M.; Mobley, D.L.

Lead Optimization Mapper: Automating Free Energy Calculations for Lead Optimization.

J. Comput.-Aided Mol. Des. 2013, 27 (9), 755–770.

DOI: 10.1007/s10822-013-9678-y

[Nguyen-2012]

Nguyen, C.N.; Young, T.K.; Gilson, M.K.

Grid Inhomogeneous Solvation Theory: Hydration Structure and Thermodynamics of the Miniature Receptor cucurbit[7]uril.

J. Chem. Phys. 2012, 137 (4), 044101.

DOI: 10.1063/1.4733951

[Xu-2019]

Xu, H.

Optimal Measurement Network of Pairwise Differences.

J. Chem. Inf. Model. 2019, 59 (11), 4720–4728.

DOI: 10.1021/acs.jcim.9b00528

[Wang-2015]

Wang, Lingle and Wu, Yujie and Deng, Yuqing and Kim, Byungchan and Pierce, Levi and Krilov, Goran and Lupyan, Dmitry and Robinson, Shaughnessy and Dahlgren, Markus K. and Greenwood, Jeremy and Romero, Donna L. and Masse, Craig and Knight, Jennifer L. and Steinbrecher, Thomas and Beuming, Thijs and Damm, Wolfgang and Harder, Ed and Sherman, Woody and Brewer, Mark and Wester, Ron and Murcko, Mark and Frye, Leah and Farid, Ramy and Lin, Teng and Mobley, David L. and Jorgensen, William L. and Berne, Bruce J. and Friesner, Richard A. and Abel, Robert

Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

J. Am. Chem. Soc., 2015, 137 (7), 2695-2703.

DOI: 10.1021/ja512751q