Determining whether a drug candidate has sufficient affinity to its target is a critical part of drug development. A purely physics-based computational method was developed that uses non-equilibrium statistical mechanics approaches alongside molecular dynamics simulations. This technique could enable researchers to accurately estimate the binding affinities of potential drug candidates.
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References
Mobley, D. L. & Gilson, M. K. Predicting binding free energies: Frontiers and benchmarks. Annu. Rev. Biophys. 46, 531–558 (2017). A review article that presents different binding free energy estimation methods.
Woo, H. J. & Roux, B. Calculation of absolute protein–ligand binding free energy from computer simulations. Proc. Natl Acad. Sci. USA 102, 6825–6830 (2005). A research article that pioneers the stratification strategy for binding affinity estimation.
Gumbart, J. C., Roux, B. & Chipot, C. Standard binding free energies from computer simulations: What is the best strategy? J. Chem. Theory Comput. 9, 794–802 (2013). A research article that implements the stratification strategy for binding affinity estimation.
Fu, H. et al. Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations. Nat. Protoc. 17, 1114–1141 (2022). A protocol article that presents the implementation of the stratification strategy for binding affinity estimation.
Govind Kumar, V., Agrawal, S., Kumar, T. K. S. & Moradi, M. Mechanistic picture for monomeric human fibroblast growth factor 1 stabilization by heparin binding. J. Phys. Chem. B 125, 12690–12697 (2021). A research article that presents a computational–experimental investigation of the hFGF1:heparin interaction.
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This is a summary of: Govind Kumar, V. et al. Binding affinity estimation from restrained umbrella sampling simulations. Nat. Comput. Sci. https://doi.org/10.1038/s43588-022-00389-9 (2022).
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Towards a purely physics-based computational binding affinity estimation. Nat Comput Sci 3, 10–11 (2023). https://doi.org/10.1038/s43588-023-00396-4
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DOI: https://doi.org/10.1038/s43588-023-00396-4
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