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Direct calculation of the binding free energies of FKBP ligands
Abstract
Direct calculations of the absolute free energies of binding for eight ligands to FKBP protein were performed using the Fujitsu BioServer massively parallel computer. Using the latest version of the general assisted model building with energy refinement (AMBER) force field for ligand model parameters and the Bennett acceptance ratio for computing free-energy differences, we obtained an excellent linear fit between the calculated and experimental binding free energies. The rms error from a linear fit is 0.4kcal∕mol for eight ligand complexes. In comparison with a previous study of the binding energies of these same eight ligand complexes, these results suggest that the use of improved model parameters can lead to more predictive binding estimates, and that these estimates can be obtained with significantly less computer time than previously thought. These findings make such direct methods more attractive for use in rational drug design.
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Citations
Cited by
Entropy-Enthalpy Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design
Chodera, J. D., & Mobley, D. L. (2013) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-083012-130318 · Cited by 531
Accurate calculation of the absolute free energy of binding for drug molecules
Aldeghi, M., Heifetz, A., Bodkin, M. J., Knapp, S., & Biggin, P. C. (2016) · Chemical Science · doi:10.1039/c5sc02678d · Cited by 347
Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?
Gumbart, J. C., Roux, B., & Chipot, C. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct3008099 · Cited by 343
Mobley, D. L., Chodera, J. D., & Dill, K. A. (2006) · The Journal of Chemical Physics · doi:10.1063/1.2221683 · Cited by 316
Predicting Absolute Ligand Binding Free Energies to a Simple Model Site
Mobley, D. L., Graves, A. P., Chodera, J. D., McReynolds, A. C., Shoichet, B. K., & Dill, K. A. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.06.002 · Cited by 310
Metadata
- Authors
- Fujitani, H., Tanida, Y., Ito, M., Jayachandran, G., Snow, C. D., Shirts, M. R., Sorin, E. J., & Pande, V. S.
- Venue
- The Journal of Chemical Physics
- Publisher
- AIP Publishing
- Published
- 2005-08-22
- Volume
- 123
- Issue
- 8
- Pages
- 084108-084108
- ISSN
- 0021-9606 (ISSN-L)
- 1089-7690
- OpenAlex
- W2070915333
- Cited by
- 187
- References
- 0
- FWCI
- 9.73
- Type
- journal article
- Language
- en
- Open access
- closed
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- Fujitani, H., Tanida, Y., Ito, M., Jayachandran, G., Snow, C. D., Shirts, M. R., Sorin, E. J., & Pande, V. S. (2005). Direct calculation of the binding free energies of FKBP ligands. The Journal of Chemical Physics. https://doi.org/10.1063/1.1999637
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