Thermodynamics

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Shin, J. H., Cuevas, L. M., Roy, R., Bonilla, S. L., Al-Hashimi, H., Greenleaf, W. J., & Herschlag, D. (2024). Exploring the energetic and conformational properties of the sequence space connecting naturally occurring RNA tetraloop receptor motifs. RNA, 30(12), 1646–1659. https://doi.org/10.1261/rna.080039.124
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Liao, J., Sergeeva, A. P., Harder, E. D., Wang, L., Sampson, J. M., Honig, B., & Friesner, R. A. (2024). A Method for Treating Significant Conformational Changes in Alchemical Free Energy Simulations of Protein–Ligand Binding. Journal of Chemical Theory and Computation, 20(19), 8609–8623. https://doi.org/10.1021/acs.jctc.4c00954
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Sampson, J. M., Cannon, D. A., Duan, J., Epstein, J. C. K., Sergeeva, A. P., Katsamba, P. S., Mannepalli, S. M., Bahna, F. A., Adihou, H., Guéret, S. M., Gopalakrishnan, R., Geschwindner, S., Rees, D. G., Sigurdardottir, A., Wilkinson, T., Dodd, R. B., De Maria, L., Mobarec, J. C., Shapiro, L., … Wang, L. (2024). Robust Prediction of Relative Binding Energies for Protein–Protein Complex Mutations Using Free Energy Perturbation Calculations. Journal of Molecular Biology, 436(16), 168640. https://doi.org/10.1016/j.jmb.2024.168640
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