ArticleJournal of computer-aided molecular design2021
A replica exchange umbrella sampling (REUS) approach to predict host-guest binding free energies in SAMPL8 challenge.
Article in Journal of computer-aided molecular design, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- Molecular dynamics simulations reveal DNA gate opening mechanisms for M. smegmatis topoisomerase 1A.Biophysical journal · 2026Article
- 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
- Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange.Journal of computer-aided molecular design · 2022Article
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Abstract
In this study, we report binding free energy calculations of various drugs-of-abuse to Cucurbit-[8]-uril as part of the SAMPL8 blind challenge. Force-field parameters were obtained from force-matching with different quantum mechanical levels of theory. The Replica Exchange Umbrella Sampling (REUS) approach was used with a cylindrical restraint to enhance the sampling of host-guest binding. Binding free energy was calculated by pulling the guest molecule from one side of the symmetric and cylindrical host, then into and through the host, and out the other side (bidirectional) as compared to pulling only to the bound pose inside the cylindrical host (unidirectional). The initial results with force-matched MP2 parameter set led to RMSE of 4.68 [Formula: see text] from experimental values. However, the follow-up study with CHARMM generalized force field parameters and force-matched PM6-D3H4 parameters resulted in RMSEs from experiment of [Formula: see text] and [Formula: see text], respectively, which demonstrates the potential of REUS for accurate binding free energy calculation given a more suitable description of energetics. Moreover, we compared the free energies for the so called bidirectional and unidirectional free energy approach and found that the binding free energies were highly similar. However, one issue in the bidirectional approach is the asymmetry of profile on the two sides of the host. This is mainly due to the insufficient sampling for these larger systems and can be avoided by longer sampling simulations. Overall REUS shows great promise for binding free energy calculations.
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