ArticleJournal of computer-aided molecular design2012
Alchemical prediction of hydration free energies for SAMPL.
Article in Journal of computer-aided molecular design, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
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- Replica Exchange of Expanded Ensembles: A Generalized Ensemble Approach with Enhanced Flexibility and Parallelizability.Journal of chemical theory and computation · 2024Article
- The Fe-MAN Challenge: Ferrates-Microkinetic Assessment of Numerical Quantum Chemistry.The journal of physical chemistry. A · 2024Article
- Evaluation of log P, pKJournal of computer-aided molecular design · 2021Article
- Energy-entropy prediction of octanol-water logP of SAMPL7 N-acyl sulfonamide bioisosters.Journal of computer-aided molecular design · 2021Article
- A fast and high-quality charge model for the next generation general AMBER force field.The Journal of chemical physics · 2020Article
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- Implementation of adaptive integration method for free energy calculations in molecular systems.PeerJ. Computer science · 2020Article
- Escaping Atom Types in Force Fields Using Direct Chemical Perception.Journal of chemical theory and computation · 2018Article
- Blinded predictions of standard binding free energies: lessons learned from the SAMPL6 challenge.Journal of computer-aided molecular design · 2018Article
- Hydration Free Energies in the FreeSolv Database Calculated with Polarized Iterative Hirshfeld Charges.Journal of chemical information and modeling · 2018Article
- Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database.Journal of chemical and engineering data · 2017Article
- Predicting water-to-cyclohexane partitioning of the SAMPL5 molecules using dielectric balancing of force fields.Journal of computer-aided molecular design · 2016Article
- Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge.Journal of computer-aided molecular design · 2016Article
- Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge.Journal of computer-aided molecular design · 2016Article
- An efficient protocol for obtaining accurate hydration free energies using quantum chemistry and reweighting from molecular dynamics simulations.Bioorganic & medicinal chemistry · 2016Article
- Calculating Partition Coefficients of Small Molecules in Octanol/Water and Cyclohexane/Water.Journal of chemical theory and computation · 2016Article
- Comparison of Methods To Reweight from Classical Molecular Simulations to QM/MM Potentials.Journal of chemical theory and computation · 2016Article
- Using MD Simulations To Calculate How Solvents Modulate Solubility.Journal of chemical theory and computation · 2016Article
- Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation.Methods in enzymology · 2016Review
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5 authors.
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Abstract
Hydration free energy calculations have become important tests of force fields. Alchemical free energy calculations based on molecular dynamics simulations provide a rigorous way to calculate these free energies for a particular force field, given sufficient sampling. Here, we report results of alchemical hydration free energy calculations for the set of small molecules comprising the 2011 Statistical Assessment of Modeling of Proteins and Ligands challenge. Our calculations are largely based on the Generalized Amber Force Field with several different charge models, and we achieved RMS errors in the 1.4-2.2 kcal/mol range depending on charge model, marginally higher than what we typically observed in previous studies (Mobley et al. in J Phys Chem B 111(9):2242-2254, 2007, J Chem Theory Comput 5(2):350-358, 2009, J Phys Chem B 115:1329-1332, 2011; Nicholls et al. in J Med Chem 51:769-779, 2008; Klimovich and Mobley in J Comput Aided Mol Design 24(4):307-316, 2010). The test set consists of ethane, biphenyl, and a dibenzyl dioxin, as well as a series of chlorinated derivatives of each. We found that, for this set, using high-quality partial charges from MP2/cc-PVTZ SCRF RESP fits provided marginally improved agreement with experiment over using AM1-BCC partial charges as we have more typically done, in keeping with our recent findings (Mobley et al. in J Phys Chem B 115:1329-1332, 2011). Switching to OPLS Lennard-Jones parameters with AM1-BCC charges also improves agreement with experiment. We also find a number of chemical trends within each molecular series which we can explain, but there are also some surprises, including some that are captured by the calculations and some that are not.
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