ArticleThe Journal of chemical physics2024
Monte Carlo simulations for free energies of hydration: Past to present.
Article in The Journal of chemical physics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
- Accurate quantum-centric simulations of intermolecular interactions.Communications physics · 2025Article
- From Implicit to Explicit: An Interaction-Reorganization Approach to Molecular Solvation Energy.Journal of chemical theory and computation · 2024Article
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- Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks [Article v0.1].Living journal of computational molecular science · 2022Article
- Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates.The journal of physical chemistry. B · 2021Article
- An explicit-solvent hybrid QM and MM approach for predicting pKa of small molecules in SAMPL6 challenge.Journal of computer-aided molecular design · 2018Article
- Quantitative surface field analysis: learning causal models to predict ligand binding affinity and pose.Journal of computer-aided molecular design · 2018Article
- Comparing alchemical and physical pathway methods for computing the absolute binding free energy of charged ligands.Physical chemistry chemical physics : PCCP · 2018Article
- Relative binding affinity prediction of farnesoid X receptor in the D3R Grand Challenge 2 using FEP.Journal of computer-aided molecular design · 2018Article
- Advances in free-energy-based simulations of protein folding and ligand binding.Current opinion in structural biology · 2016Review
- Distinguishing binders from false positives by free energy calculations: fragment screening against the flap site of HIV protease.The journal of physical chemistry. B · 2015Article
- Sampling of Organic Solutes in Aqueous and Heterogeneous Environments Using Oscillating Excess Chemical Potentials in Grand Canonical-like Monte Carlo-Molecular Dynamics Simulations.Journal of chemical theory and computation · 2014Article
- Funnel metadynamics as accurate binding free-energy method.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Biomolecular electrostatics and solvation: a computational perspective.Quarterly reviews of biophysics · 2012Review
- Conformational change of the methionine 20 loop of Escherichia coli dihydrofolate reductase modulates pKa of the bound dihydrofolate.Protein science : a publication of the Protein Society · 2007Article
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1 author.
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Abstract
A summary of the development of Monte Carlo statistical mechanics simulations for the computation of free energies of hydration of organic molecules is followed by presentation of results with the latest version of the optimized potentials for liquid simulations-all atom force field and the TIP4P water model. Scaling of the Lennard-Jones interactions between water, oxygen, and carbon atoms by a factor of 1.25 is found to improve the accuracy of free energies of hydration for 50 prototypical organic molecules from a mean unsigned error of 1.0-1.2 to 0.4 kcal/mol.
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