ArticleJournal of computer-aided molecular design2016
Blinded predictions of distribution coefficients in the SAMPL5 challenge.
Article in Journal of computer-aided molecular design, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- SAMPL7 blind challenge: quantum-mechanical prediction of partition coefficients and acid dissociation constants for small drug-like molecules.Journal of computer-aided molecular design · 2021Article
- Best Practices for Alchemical Free Energy Calculations [Article v1.0].Living journal of computational molecular science · 2020Article
- Blinded predictions of standard binding free energies: lessons learned from the SAMPL6 challenge.Journal of computer-aided molecular design · 2018Article
- Metabolism and hydrophilicity of the polarised 'Janus face' all-Chemical science · 2018Article
- Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations.Journal of computer-aided molecular design · 2018Article
- Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge.Journal of computer-aided molecular design · 2017Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
In the context of the SAMPL5 challenge water-cyclohexane distribution coefficients for 53 drug-like molecules were predicted. Four different models based on molecular dynamics free energy calculations were tested. All models initially assumed only one chemical state present in aqueous or organic phases. Model A is based on results from an alchemical annihilation scheme; model B adds a long range correction for the Lennard Jones potentials to model A; model C adds charging free energy corrections; model D applies the charging correction from model C to ionizable species only. Model A and B perform better in terms of mean-unsigned error ([Formula: see text] D units - 95 % confidence interval) and determination coefficient [Formula: see text], while charging corrections lead to poorer results with model D ([Formula: see text] and [Formula: see text]). Because overall errors were large, a retrospective analysis that allowed co-existence of ionisable and neutral species of a molecule in aqueous phase was investigated. This considerably reduced systematic errors ([Formula: see text] and [Formula: see text]). Overall accurate [Formula: see text] predictions for drug-like molecules that may adopt multiple tautomers and charge states proved difficult, indicating a need for methodological advances to enable satisfactory treatment by explicit-solvent molecular simulations.
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