ArticleJournal of computer-aided molecular design2018
SAMPL6 host-guest blind predictions using a non equilibrium alchemical approach.
Article in Journal of computer-aided molecular design, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Solvation Free Energies of Drug-like Molecules via Fast Growth in an Explicit Solvent: Assessment of the AM1-BCC, RESP/HF/6-31G*, RESP-QM/MM, and ABCG2 Fixed-Charge Approaches.Journal of chemical theory and computation · 2025Article
- Host Dynamics under General-Purpose Force Fields.Molecules (Basel, Switzerland) · 2023Article
- Relative Binding Free Energy between Chemically Distant Compounds Using a Bidirectional Nonequilibrium Approach.Journal of chemical theory and computation · 2022Article
- Virtual Double-System Single-Box for Absolute Dissociation Free Energy Calculations in GROMACS.Journal of chemical information and modeling · 2021Article
- Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches.Communications chemistry · 2021Article
- SAMPL7 TrimerTrip host-guest binding poses and binding affinities from spherical-coordinates-biased simulations.Journal of computer-aided molecular design · 2021Article
- SAMPL7 TrimerTrip host-guest binding affinities from extensive alchemical and end-point free energy calculations.Journal of computer-aided molecular design · 2021Article
- SAMPL7 blind predictions using nonequilibrium alchemical approaches.Journal of computer-aided molecular design · 2021Article
- Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software.Journal of computer-aided molecular design · 2021Article
- SAMPL7: Host-guest binding prediction by molecular dynamics and quantum mechanics.Journal of computer-aided molecular design · 2021Article
- Virtual Double-System Single-Box: A Nonequilibrium Alchemical Technique for Absolute Binding Free Energy Calculations: Application to Ligands of the SARS-CoV-2 Main Protease.Journal of chemical theory and computation · 2020Article
- Upgraded AMBER Force Field for Zinc-Binding Residues and Ligands for Predicting Structural Properties and Binding Affinities in Zinc-Proteins.ACS omega · 2020Article
- A remark on the efficiency of the double-system/single-box nonequilibrium approach in the SAMPL6 SAMPLing challenge.Journal of computer-aided molecular design · 2020Article
- SAMPL6 host-guest binding affinities and binding poses from spherical-coordinates-biased simulations.Journal of computer-aided molecular design · 2020Article
- SAMPL6 blind predictions of water-octanol partition coefficients using nonequilibrium alchemical approaches.Journal of computer-aided molecular design · 2020Article
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3 authors.
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Abstract
In this paper, we compute, by means of a non equilibrium alchemical technique, called fast switching double annihilation methods (FSDAM), the absolute standard dissociation free energies of the the octa acids host-guest systems in the SAMPL6 challenge initiative. FSDAM is based on the production of canonical configurations of the bound and unbound states via enhanced sampling and on the subsequent generation of hundreds of fast non-equilibrium ligand annihilation trajectories. The annihilation free energies of the ligand when bound to the receptor and in bulk solvent are obtained from the collection of work values using an estimate based on the Crooks theorem for driven non equilibrium processes. The FSDAM blind prediction, relying on the normality assumption for the annihilation work distributions, ranked fairly well among the submitted blind predictions that were not adjusted with a linear corrections obtained from retrospective data on similar host guest systems. Improved results for FSDAM can be obtained by post-processing the work data assuming mixtures of normal components.
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