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Alchemical Enhanced Sampling with Optimized Phase Space Overlap

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Synergistic Effect of Small Molecular Organic Matter and Functional Groups in Coal on Methane Adsorption

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Binding Thermodynamics of Fourth-Generation EGFR Inhibitors Revealed by Absolute Binding Free Energy Calculations

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Uncovering the Mechanism of Drug Resistance Caused by the T790M Mutation in EGFR Kinase From Absolute Binding Free Energy Calculations

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Essential Considerations for Free Energy Calculations of RNA–Small Molecule Complexes: Lessons from the Theophylline-Binding RNA Aptamer

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One for All, All for One: A Unified Framework for Free-Energy Calculations

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Convergence-Adaptive Roundtrip Method Enables Rapid and Accurate FEP Calculations

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Accelerating and Automating the Free Energy Perturbation Absolute Binding Free Energy Calculation with the RED-E Function

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Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints

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An Automated On-The-Fly Optimization of Resource Allocation for High-Throughput Protein-Ligand Binding Free Energy SimulationsPreprint

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Absolute binding energy calculation supported with metadynamic simulation and molecular dynamics improves inhibitors identification against GSK3-β for glaucoma treatment

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Mutation-Dependent Conformational Dynamics and Dual-Mode Afatinib Binding in EGFR Exon 19 Variants

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Computational Evaluation of Peptide–Protein Binding Affinities: Application of Potential of Mean Force Calculations to SH2 Domains

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Flexible framework of computing binding free energy using the energy representation theory of solution

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Structural Insights into the Roles of PARP4 and NAD + in the Human Vault CagePreprint

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A nonequilibrium alchemical method for drug-receptor absolute binding free energy calculations: the role of restraintsPreprint

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Assessment of the Topology and OligomerisationStates of Coiled Coils Using Metadynamics withConformational RestraintsPreprint

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Evaluating Nirmatrelvir Resistance in SARS-CoV-2 Main Protease: A Comparison Between MM/PBSA and Free Energy Perturbation

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Computational Binding Affinities of Disheveled PDZ Protein-Ligand ComplexesPreprint

Singh, A., Kancharla, H., Jubintoro, A., Blankenberg, P. M., & Zheng, J. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.09.21.672002

Relative BAT: An Automated Tool for Relative Binding Free Energy Calculations by the Separated Topologies Approach

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Thermodynamic and Kinetic Analysis of Molecular Conformational Dynamics in a Riemannian Framework

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Elucidating the Role of Protein–Protein Interactions in Modulating Inhibitor Affinity and Release Mechanisms in Serine Arginine Protein Kinase

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Mutation-Driven Remodeling of the LRRK2 Kinase Free-Energy Landscape and Its Consequences for Conformational Transitions and Inhibitor Binding Affinity

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BFEE-Docking: A User-Friendly and Customizable End-to-End Tool from High-Throughput Virtual Screening to Binding Free-Energy Calculations

Sun, X., Li, Z., Shao, X., Cai, W., Li, Z., & Fu, H. (2026) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.6c00830

A Force-Kernel Reformulation of the Extended-System Adaptive Biasing Force for Free-Energy Calculations

Kang, C., Verma, R., Sonpal, A., Shoji, A., Chipot, C. J., & Pfaendtner, J. (2026) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.6c00879

Alchemical Free-Energy Framework for Multiresidue Reoptimization of Antimicrobial Peptide-Membrane Affinity

Tian, C., Zhou, M., Wang, H., Jinbo, Y., Shao, X., & Cai, W. (2026) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.6c01030

BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-Energy Calculations

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BPS2026 – CHARMM-GUI free-energy calculator 2 for protein-ligand binding free-energy simulations

Suh, D., & Im, W. (2026) · Biophysical Journal · doi:10.1016/j.bpj.2025.11.2079

Standard Binding Free-Energy Calculations: How Far Are We from Automation?

Fu, H., Chipot, C. J., Shao, X., & Cai, W. (2023) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.3c04370 · Cited by 18 · see citing works

Automated Assessment of Binding Affinity via Alchemical Free Energy CalculationsPreprint

Kuhn, M., Firth‐Clark, S., Tosco, P., Mey, A. S. J. S., Mackey, M., & Michel, J. (2020) · ChemRxiv · doi:10.26434/chemrxiv.11812053 · Cited by 1 · see citing works

CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER

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