ArticleJournal of computer-aided molecular design2014
The SAMPL4 hydration challenge: evaluation of partial charge sets with explicit-water molecular dynamics simulations.
Article in Journal of computer-aided molecular design, 2014. 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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Who cites it
19 citing papers in PubMed.
- Machine-Learned Electrostatic Potentials for Accurate Hydration Free Energy Calculations.Journal of chemical theory and computation · 2026Article
- Elucidating the Solvent-Dependent Solvation and Structural Stability of Irinotecan: A Molecular Simulation Study.Chemphyschem : a European journal of chemical physics and physical chemistry · 2026Article
- A Graph Neural Network Charge Model Targeting Accurate Electrostatic Properties of Organic Molecules.Journal of chemical theory and computation · 2025Article
- Prediction of toluene/water partition coefficients of SAMPL9 compounds: comparison of the molecular dynamics force fields GAFF/RESP and GAFF/IPolQ-Mod + LJ-fit.Physical chemistry chemical physics : PCCP · 2024Article
- What is the Optimal Dipole Moment for Nonpolarizable Models of Liquids?Journal of chemical theory and computation · 2023Article
- Improving Force Field Accuracy by Training against Condensed-Phase Mixture Properties.Journal of chemical theory and computation · 2022Article
- Article
- A deep learning approach for the blind logP prediction in SAMPL6 challenge.Journal of computer-aided molecular design · 2020Article
- SAMPL6 Octanol-water partition coefficients from alchemical free energy calculations with MBIS atomic charges.Journal of computer-aided molecular design · 2020Article
- Non-bonded force field model with advanced restrained electrostatic potential charges (RESP2).Communications chemistry · 2020Article
- Applicability of a thermodynamic cycle approach for a force field parametrization targeting non-aqueous solvation free energies.Journal of computer-aided molecular design · 2020Article
- Data-driven analysis of the number of Lennard-Jones types needed in a force field.Communications chemistry · 2020Article
- GAFF/IPolQ-Mod+LJ-Fit: Optimized force field parameters for solvation free energy predictions.ADMET & DMPK · 2020Article
- An explicit-solvent hybrid QM and MM approach for predicting pKa of small molecules in SAMPL6 challenge.Journal of computer-aided molecular design · 2018Article
- Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database.Journal of chemical and engineering data · 2017Article
- Bayesian Model Averaging for Ensemble-Based Estimates of Solvation-Free Energies.The journal of physical chemistry. B · 2017Article
- Determination of the binding mode for anti-inflammatory natural product xanthohumol with myeloid differentiation protein 2.Drug design, development and therapy · 2016Article
- Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge.Journal of computer-aided molecular design · 2014Article
- Blind prediction of solvation free energies from the SAMPL4 challenge.Journal of computer-aided molecular design · 2014Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
We used blind predictions of the 47 hydration free energies in the SAMPL4 challenge to test multiple partial charge models in the context of explicit solvent free energy simulations with the general AMBER force field. One of the partial charge models, IPolQ-Mod, is a fast continuum solvent-based implementation of the IPolQ approach. The AM1-BCC, restrained electrostatic potential (RESP) and IpolQ-Mod approaches all perform reasonably well (R(2) > 0.8), while VCharge, though faster, gives less accurate results (R(2) of 0.5). The AM1-BCC results are more accurate than those of RESP for tertiary amines and nitrates, but the overall difference in accuracy between these methods is not statistically significant. Interestingly, the IPolQ-Mod method is found to yield partial charges in very close agreement with RESP. This observation suggests that the success of RESP may be attributed to its fortuitously approximating the arguably more rigorous IPolQ approach.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.