ArticleJournal of computer-aided molecular design2022
Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange.
Article in Journal of computer-aided molecular design, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- Expanded ensemble predictions of absolute binding free energies in the SAMPL9 host-guest challenge.Physical chemistry chemical physics : PCCP · 2023Article
- An overview of the SAMPL8 host-guest binding challenge.Journal of computer-aided molecular design · 2022Article
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3 authors.
Funding
Abstract
Umbrella sampling along a one-dimensional order parameter in combination with Hamiltonian replica exchange was employed to calculate the binding free energy of five guest molecules with known affinity to cucurbit[8]uril. A simple empirical approach correcting for the overestimation of the affinity by the GAFF force field was proposed and subsequently applied to the seven guest molecules of the "Drugs of Abuse" SAMPL8 challenge. Compared to the uncorrected binding free energies, the systematic error decreased but quantitative agreement with experiment was only reached for a few compounds. From a retrospective analysis a weak point of the correction term was identified.
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