ArticleJournal of computer-aided molecular design2018
Blinded predictions of standard binding free energies: lessons learned from the SAMPL6 challenge.
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 7 papers.
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Who cites it
7 citing papers in PubMed.
- Comparison of Methodologies for Absolute Binding Free Energy Calculations of Ligands to Intrinsically Disordered Proteins.Journal of chemical theory and computation · 2024Article
- Automated Adaptive Absolute Binding Free Energy Calculations.Journal of chemical theory and computation · 2024Article
- Comparison of Receptor-Ligand Restraint Schemes for Alchemical Absolute Binding Free Energy Calculations.Journal of chemical theory and computation · 2023Article
- Local Ion Densities can Influence Transition Paths of Molecular Binding.Frontiers in molecular biosciences · 2022Article
- Accurate Receptor-Ligand Binding Free Energies from Fast QM Conformational Chemical Space Sampling.International journal of molecular sciences · 2021Article
- The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations.Journal of computer-aided molecular design · 2020Article
- Binding Thermodynamics of Host-Guest Systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative.Journal of chemical theory and computation · 2019Article
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Authors and funding
3 authors.
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Abstract
In the context of the SAMPL6 challenges, series of blinded predictions of standard binding free energies were made with the SOMD software for a dataset of 27 host-guest systems featuring two octa-acids hosts (OA and TEMOA) and a cucurbituril ring (CB8) host. Three different models were used, ModelA computes the free energy of binding based on a double annihilation technique; ModelB additionally takes into account long-range dispersion and standard state corrections; ModelC additionally introduces an empirical correction term derived from a regression analysis of SAMPL5 predictions previously made with SOMD. The performance of each model was evaluated with two different setups; buffer explicitly matches the ionic strength from the binding assays, whereas no-buffer merely neutralizes the host-guest net charge with counter-ions. ModelC/no-buffer shows the lowest mean-unsigned error for the overall dataset (MUE 1.29 < 1.39 < 1.50 kcal mol
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