Free energy perturbation simulations measure the change in binding affinity of the Aβ25–35 peptide to the zwitterionic bilayer caused by oxidation. Luo, X., Khayat, E., Bowers, S. R., Delfing, B. M., Lockhart, C., & Klimov, D. K. (2025) Free energy perturbation simulations measure the change in binding affinity of the Aβ25–35 peptide to the zwitterionic bilayer caused by oxidation. J. Chem. Inf. Model. (accepted) >
Applying absolute free energy perturbation molecular dynamics to diffusively binding ligands. Laracuente, X. E., Delfing, B. M., Luo, X., Olson, A., Jeffries, W., Bowers, S. R., Foreman, K. W., Lee, K.-H., Paige, M., Kehn-Hall, K., Lockhart, C., & Klimov, D. K. (2025) Applying absolute free energy perturbation molecular dynamics to diffusively binding ligands. J. Chem. Theory Comput. 21(8): 4286-4298, doi: 10.1021/acs.jctc.5c00121
Can free energy perturbation simulations coupled with replica-exchange molecular dynamics study ligands with distributed binding sites? Lockhart, C., Luo, X., Olson, A., Delfing, B. M., Laracuente, X., Foreman, K. W., Paige, M., Kehn-Hall, K., & Klimov, D. K. (2023) Can free energy perturbation simulations coupled with replica-exchange molecular dynamics study ligands with distributed binding sites? J. Chem. Inf. Model. 63(15): 4791-4802, doi: 10.1021/acs.jcim.3c00631