Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations

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RVX-208

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Does a More Precise Chemical Description of Protein–Ligand Complexes Lead to More Accurate Prediction of Binding Affinity?

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Estimating the Roles of Protonation and Electronic Polarization in Absolute Binding Affinity Simulations

King, E. J., Qi, R., Li, H., Luo, R., & Aitchison, E. W. (2021) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.0c01305 · Cited by 15 · see citing works

On Restraints in End‐Point Protein–Ligand Binding Free Energy Calculations

Menzer, W. M., Xie, B., & Minh, D. D. L. (2019) · Journal of Computational Chemistry · doi:10.1002/jcc.26119 · Cited by 16 · see citing works

Equilibrium and Nonequilibrium Ensemble Methods for Accurate, Precise and Reproducible Absolute Binding Free Energy Calculations

Bhati, A. P., Wan, S., & Coveney, P. (2024) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.4c01389 · Cited by 13 · see citing works

Quantification of the Impact of Structure Quality on Predicted Binding Free Energy Accuracy

Behera, S., Hahn, D. F., Wilson, C. J., Marsili, S., Tresadern, G., Gapsys, V., & de Groot, B. L. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5c00947 · Cited by 14 · see citing works

In Silico Prediction of Ligand Binding Energies in Multiple Therapeutic Targets and Diverse Ligand Sets—A Case Study on BACE1, TYK2, HSP90, and PERK Proteins

Frush, E. H., Sekharan, S., & Keinan, S. (2017) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.7b07224 · Cited by 14 · see citing works

The role of loop dynamics in the prediction of ligand–protein binding enthalpy

Çınaroğlu, S. S., & Biggin, P. C. (2023) · Chemical Science · doi:10.1039/d2sc06471e · Cited by 13 · see citing works

Discovery of highly potent phosphodiesterase-1 inhibitors by a combined-structure free energy perturbation approach

Li, Z., Jiang, M., Liu, R., Wang, Q., Zhou, Q., Huang, Y., Wu, Y., Zhan, C., & Luo, H. (2024) · Acta Pharmaceutica Sinica B · doi:10.1016/j.apsb.2024.06.021 · Cited by 12 · see citing works

Deciphering Selectivity Mechanism of BRD9 and TAF1(2) toward Inhibitors Based on Multiple Short Molecular Dynamics Simulations and MM-GBSA Calculations

Wang, L., Wang, Y., Yu, Y. X., Liu, D., Zhao, J., & Zhang, L. (2023) · Molecules · doi:10.3390/molecules28062583 · Cited by 12 · see citing works

Energetic Fingerprinting of Ligand Binding to Paralogous Proteins: The Case of the Apoptotic Pathway

Ivanov, S. M., Huber, R. G., Alibay, I., Warwicker, J., & Bond, P. J. (2018) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.8b00765 · Cited by 12 · see citing works

Predicting Ligand Selectivity Across Bromodomain Families

Aldeghi, M., Heifetz, A., Bodkin, M. J., Knapp, S., & Biggin, P. C. (2016) · Biophysical Journal · doi:10.1016/j.bpj.2015.11.2915

Absolute Binding Free Energy Calculations of Bromodomain Inhibitors

Aldeghi, M., Knapp, S., Heifetz, A., Barker, J. J., Bodkin, M. J., Law, R. J., & Biggin, P. C. (2015) · Biophysical Journal · doi:10.1016/j.bpj.2014.11.1954

D-MBIS Nonbonded Force Field Parameters Improve Specificity and Selectivity Prediction in Bromodomains

Macaya, L., & Vöhringer‐Martinez, E. (2026) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.6c00354

Rapid and Reliable Binding Affinity Prediction of Bromodomain Inhibitors: A Computational Study

Wan, S., Bhati, A. P., Zasada, S. J., Wall, I. D., Green, D. V. S., Bamborough, P., & Coveney, P. V. (2016) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.6b00794 · Cited by 76 · see citing works

A critical review of validation, blind testing, and real-world use of alchemical protein-ligand binding free energy calculations

Abel, R., Wang, L., Mobley, D. L., & Friesner, R. A. (2017) · Current Topics in Medicinal Chemistry · doi:10.2174/1568026617666170414142131 · Cited by 101 · see citing works