FEP+ References

1.

Lu, C.; Wu, C.; Ghoreishi, D.; Chen, W.; Wang, L.; Damm, W.; Ross, G. A.; Dahlgren, M. K.; Russell, E.; Von Bargen, C. D.; Abel, R.; Friesner. R. A.; Harder, E.; OPLS4: Improving Force Field Accuracy on Challenging Regimes of Chemical Space. J. Chem. Theory Comput. 2021, 17, 4291.

2.

Harder, E.; Damm, W.; Maple, J.; Wu, C.; Reboul, M.; Xiang, J. Y.; Wang, L.; Lupyan, D.; Dahlgren, M. K.; Knight, J. L.; Kaus,J. W.; Cerutti, D. S.; Krilov, G.; Jorgensen, W. L.; Abel, R.; Friesner. R. A. OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins. J. Chem. Theory Comput.2016, 12, 281.

3.

Liu, P.; Kim, B.; Friesner, R. A.; Berne, B. J., Replica exchange with solute tempering: a method for sampling biological systems in explicit water. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 13749.

4.

Wang, L.; Friesner, R. A.; Berne, B. J. Replica Exchange with Solute Scaling: A More Efficient Version of Replica Exchange with Solute Tempering (REST2). J. Phys. Chem. B 2011, 115, 9431.

5.

Wang, L.; Berne, B. J.; Friesner, R. A. On achieving high accuracy and reliability in the calculation of relative protein–ligand binding affinities. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 1937.

6.

Wang, L.; Wu, Y.; Deng, Y.; Kim, B.; Pearce, L.; Krilov G.; Lupyan, D.; Robinson, S.; Dahlgren, M. K.; Greenwood, J.; Romero, D. L.; Masse, C.; Knight, J. L.; Steinbrecher, T.; Beuming, T.; Damm, W.; Harder, E.; Sherman, W.; Brewer, M.; Wester, R.; Murcko, M.; Frye, L.; Farid, R.; Lin, T.; Mobley D. L.; Jorgensen, W. L.; Berne, B. J.; Friesner, R. A.; Abel, R. 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, 2695.

7.

Wang, L.; Deng, Y.; Knight, J. L.; Wu, Y.; Kim, B.; Sherman, W.; Shelley, J.; Lin, T.; Abel, R. Modeling Local Structural Rearrangements Using FEP/REST: Application to Relative Binding Affinity Predictions of CDK2 Inhibitors. J. Chem. Theory Comput. 2013, 9, 1282.

8.

Chen, W.; Deng, Y.; Russell, E.; Wu, Y.; Abel, R.; Wang, L. Accurate Calculation of Relative Binding Free Energies between Ligands with Different Net Charges. J. Chem. Theory Comput. 2018, 14, 6346.

9.

de Oliveira, C.; Yu, H. S.; Chen, W.; Abel, R.; Wang, L. Rigorous Free Energy Perturbation Approach to Estimating Relative Binding Affinities between Ligands with Multiple Protonation and Tautomeric States. J. Chem. Theory Comput. 2019, 15, 424. DOI: 10.1021/acs.jctc.8b00826

10.

Zwanzig, R. W., High-temperature equation of state by a perturbation method. 1. Nonpolar gases. J. Chem. Phys. 1954, 22, 1420.

11.

Bennett, C. H., Efficient Estimation of Free Energy Differences from Monte Carlo Data. J. Comp. Phys. 1976, 22, 245.

12.

Abel, R.; Wang, L.; Mobley, D. L.; Friesner. R. A. OPLS3: A Critical Review of Validation,Blind Testing, and Real-World Use of Alchemical Protein-Ligand Binding Free Energy Calculations. Curr. Top. Med. Chem. 2017, 17, 2577.

13.

Huang, Y.; Chen, W.; Wallace, J. A.; Shen, J. All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water. J. Chem. Theory Comput. 2016, 12, 5411.

14.

de Oliveira, C.; Leswing, K.; Feng, S.; Kanters, R.; Abel, R.; Bhat, S. FEP Protocol Builder: Optimization of Free Energy Perturbation Protocols Using Active Learning. J. Chem. Inf. Model.2023, 63, 5592. DOI: 10.1021/acs.jcim.3c00681

15.

Sampson, J. M.; Cannon, D. A.; Duan, J.; Epstein, J. K.; Sergeeva, A. P.; Katsamba, P. S.; Mannepali, S. M.; Bahna, F. A.; Adihou, H.; Guéret, A. M.; Gopalakrishan, R.; Geschwindner, S.; Rees, D. G.; Sigurdardottir, A; Wilkinson, T.; Dodd, R. B.; De Maria, L.; Mobarec, J. C.; Shapiro, L.; Honig, B.; Wang, L. Robust Prediction of Relative Binding Energies for Protein–Protein Complex Mutations Using Free Energy Perturbation Calculations. J. Mol. Bio.2024, 436, 168640. DOI: 10.1016/j.jmb.2024.168640 Note: FMP files from this paper can be downloaded here (340 MB).