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CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application

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Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation

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Let’s get honest about sampling

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Distinguishing Binders from False Positives by Free Energy Calculations: Fragment Screening Against the Flap Site of HIV Protease

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Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo

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Application of the G-JF discrete-time thermostat for fast and accurate molecular simulations

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Symmetry Numbers for Rigid, Flexible, and Fluxional Molecules: Theory and Applications

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Binding of divalent cations to acetate: molecular simulations guided by Raman spectroscopy

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Assessment of the PETase conformational changes induced by poly(ethylene terephthalate) binding

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Probing Carbohydrate Product Expulsion from a Processive Cellulase with Multiple Absolute Binding Free Energy Methods

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Free Energy Methods in Drug Discovery—Introduction

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A generic implementation of replica exchange with solute tempering (REST2) algorithm in NAMD for complex biophysical simulations

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Entropic Cost of Protein−Ligand Binding and Its Dependence on the Entropy in Solution

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Computing Relative Binding Affinity of Ligands to Receptor: An Effective Hybrid Single-Dual Topology Free Energy Perturbation Approach in NAMD

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Evaluating the use of absolute binding free energy in the fragment optimisation process

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Absolute Alchemical Free Energy Calculations for Ligand Binding: A Beginner's Guide.

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Absolute FKBP binding affinities obtained via nonequilibrium unbinding simulations

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Discovery of Novel Human Aquaporin-1 Blockers

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Functional Hydration and Conformational Gating of Proton Uptake in Cytochrome c Oxidase

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Leveraging Symmetries of Static Atomic Multipole Electrostatics in Molecular Dynamics Simulations.

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A Streamlined, General Approach for Computing Ligand Binding Free Energies and Its Application to GPCR-Bound Cholesterol

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Blind Prediction of Charged Ligand Binding Affinities in a Model Binding Site

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Challenges Encountered Applying Equilibrium and Nonequilibrium Binding Free Energy Calculations

Baumann, H. M., Gapsys, V., de Groot, B. L., & Mobley, D. L. (2021) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.0c10263 · Cited by 58 · see citing works

Chemical potential of liquids and mixtures via adaptive resolution simulation

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An overview of the SAMPL8 host–guest binding challenge

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Accounting for ligand conformational restriction in calculations of protein-ligand binding affinities.

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Elucidating the Energetics of Entropically Driven Protein–Ligand Association: Calculations of Absolute Binding Free Energy and Entropy

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Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis

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Molecular Mechanism of Ion-Ion and Ion-Substrate Coupling in the Na+-Dependent Leucine Transporter LeuT

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Advances in uncovering the mechanisms of macromolecular conformational entropy

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Absolute binding free energy calculations of sparsomycin analogs to the bacterial ribosome.

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Computation of the binding affinities of catechol‐O‐methyltransferase inhibitors: Multisubstate relative free energy calculations

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Application of a polarizable force field to calculations of relative protein–ligand binding affinities

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Structure and Mechanism of Human UDP-xylose Synthase

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Separated topologies--a method for relative binding free energy calculations using orientational restraints.

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Physics-based methods for studying protein-ligand interactions.

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Insight into the Structural Deformations of Beta-Cyclodextrin Caused by Alcohol Cosolvents and Guest Molecules

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Building intuition for binding free energy calculations: Bound state definition, restraints, and symmetry

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Small Molecule Solvation Free Energy: Enhanced Conformational Sampling Using Expanded Ensemble Molecular Dynamics Simulation

Paluch, A. S., Mobley, D. L., & Maginn, E. J. (2011) · Journal of Chemical Theory and Computation · doi:10.1021/ct200377w · Cited by 46 · see citing works

Best practices in free energy calculations for drug design.

Shirts, M. (2012) · Methods in molecular biology · doi:10.1007/978-1-61779-465-0_26 · Cited by 48 · see citing works

Molecular dynamics modeling of tubulin C‐terminal tail interactions with the microtubule surface

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Statistical Mechanics of Ligand–Receptor Noncovalent Association, Revisited: Binding Site and Standard State Volumes in Modern Alchemical Theories

Procacci, P., & Chelli, R. (2017) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.6b01192 · Cited by 45 · see citing works

Insights from molecular dynamics and DFT calculations into the interaction of 1,4-benzodiazepines with 2-hydroxypropyl-βCD in a theoretical study

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Ligand Binding Free Energies with Adaptive Water Networks: Two-Dimensional Grand Canonical Alchemical Perturbations

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Separated topologies--a method for relative binding free energy calculations using orientational restraints.

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Accurate Estimation of Protein-ligand Binding Free Energies Based on Geometric Restraints

Fu, H., Chen, H., Zhang, H., Shao, X., & Cai, W. (2021) · 化学学报 · doi:10.6023/a20100489 · Cited by 1 · see citing works

Comparison of Receptor–Ligand Restraint Schemes for Alchemical Absolute Binding Free Energy Calculations

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Binding Free Energy Calculation of Small Molecules to Rna with Multiple Binding Poses

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Extending the scope of alchemical perturbation methods for ligand binding free energy calculations

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