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- W1995800242 abstract "Traditional free energy calculations are known for their issues with scalability, speed and convergence. We have recently developed the biasing potential replica exchange multi-site λ-dynamics (BP-REX MSλD) method, which is a free energy method capable of transforming multiple substituents at multiple sites on a common framework with relative ease. With this methodology, we are able to show convergence of flexible moieties for symmetric benzoquinone derivatives, and have developed a series of metrics capable of increasing the λ-space sampling. We grouped and ordered the substituents based on volume occupancy, and were able to compute the free energy of binding for a series of challenging geldanamycin-derivatives for heat shock protein 90. The perturbations spanned by as much as 60 A3 and we were able to model these with a 2.4 kcal/mol average unsigned error. These metrics coupled with BP-REX MSλD allow for routine calculations on the order of hundreds of compounds in a few simulations." @default.
- W1995800242 created "2016-06-24" @default.
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- W1995800242 date "2015-01-01" @default.
- W1995800242 modified "2023-09-30" @default.
- W1995800242 title "Biasing Potential Replica Exchange Multi-Site λ-Dynamics for Efficient Free Energy Calculations of Protein-Ligand Interactions" @default.
- W1995800242 doi "https://doi.org/10.1016/j.bpj.2014.11.1951" @default.
- W1995800242 hasPublicationYear "2015" @default.
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