ArticleJournal of computer-aided molecular design2017
Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge.
Article in Journal of computer-aided molecular design, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed.
- An Evaluation of the Interaction of Brefeldin A with Mitogen-Activated Protein Kinase 1 (MAPK1) and Protein Kinase C Alpha (PrKCα): Insights from Molecular Modelling Studies.International journal of molecular sciences · 2026Article
- Automated Adaptive Absolute Binding Free Energy Calculations.Journal of chemical theory and computation · 2024Article
- Calculation of protein-ligand binding entropies using a rule-based molecular fingerprint.Biophysical journal · 2024Article
- Comparison of Receptor-Ligand Restraint Schemes for Alchemical Absolute Binding Free Energy Calculations.Journal of chemical theory and computation · 2023Article
- The role of water in host-guest interaction.Nature communications · 2021Article
- Data-Driven Mapping of Gas-Phase Quantum Calculations to General Force Field Lennard-Jones Parameters.Journal of chemical theory and computation · 2020Article
- Effect of set up protocols on the accuracy of alchemical free energy calculation over a set of ACK1 inhibitors.PloS one · 2019Article
- Detailed potential of mean force studies on host-guest systems from the SAMPL6 challenge.Journal of computer-aided molecular design · 2018Article
- Blinded predictions of standard binding free energies: lessons learned from the SAMPL6 challenge.Journal of computer-aided molecular design · 2018Article
- Overview of the SAMPL6 host-guest binding affinity prediction challenge.Journal of computer-aided molecular design · 2018Article
- Bind3P: Optimization of a Water Model Based on Host-Guest Binding Data.Journal of chemical theory and computation · 2018Article
- Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations.Journal of computer-aided molecular design · 2018Article
- HYDROPHOBE Challenge: A Joint Experimental and Computational Study on the Host-Guest Binding of Hydrocarbons to Cucurbiturils, Allowing Explicit Evaluation of Guest Hydration Free-Energy Contributions.The journal of physical chemistry. B · 2017Article
- Predicting Binding Free Energies: Frontiers and Benchmarks.Annual review of biophysics · 2017Review
- Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database.Journal of chemical and engineering data · 2017Article
- The SAMPL5 host-guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method.Journal of computer-aided molecular design · 2017Article
- Overview of the SAMPL5 host-guest challenge: Are we doing better?Journal of computer-aided molecular design · 2017Review
- Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge.Journal of computer-aided molecular design · 2016Article
- Blinded predictions of distribution coefficients in the SAMPL5 challenge.Journal of computer-aided molecular design · 2016Article
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3 authors.
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Abstract
In the context of the SAMPL5 blinded challenge standard free energies of binding were predicted for a dataset of 22 small guest molecules and three different host molecules octa-acids (OAH and OAMe) and a cucurbituril (CBC). Three sets of predictions were submitted, each based on different variations of classical molecular dynamics alchemical free energy calculation protocols based on the double annihilation method. The first model (model A) yields a free energy of binding based on computed free energy changes in solvated and host-guest complex phases; the second (model B) adds long range dispersion corrections to the previous result; the third (model C) uses an additional standard state correction term to account for the use of distance restraints during the molecular dynamics simulations. Model C performs the best in terms of mean unsigned error for all guests (MUE [Formula: see text]-95 % confidence interval) for the whole data set and in particular for the octa-acid systems (MUE [Formula: see text]). The overall correlation with experimental data for all models is encouraging ([Formula: see text]). The correlation between experimental and computational free energy of binding ranks as one of the highest with respect to other entries in the challenge. Nonetheless the large MUE for the best performing model highlights systematic errors, and submissions from other groups fared better with respect to this metric.
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