ReviewJournal of computer-aided molecular design2014
Blind prediction of solvation free energies from the SAMPL4 challenge.
Review 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 84 papers.
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Who cites it
84 citing papers in PubMed.
- The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling.The journal of physical chemistry. B · 2024Article
- Calculations of Absolute Solvation Free Energies with Transformato─Application to the FreeSolv Database Using the CGenFF Force Field.Journal of chemical theory and computation · 2023Article
- Persistent Dirac for molecular representation.Scientific reports · 2023Article
- Molecular Property Prediction of Modified Gedunin Using Machine Learning.Molecules (Basel, Switzerland) · 2023Article
- Implementation and Optimization of the Embedded Cluster Reference Interaction Site Model with Atomic Charges.The journal of physical chemistry. A · 2022Article
- Performing Molecular Dynamics Simulations and Computing Hydration Free Energies on the B3LYP-D3(BJ) Potential Energy Surface with Adaptive Force Matching: A Benchmark Study with Seven Alcohols and One Amine.ACS physical chemistry Au · 2021Article
- Automated high throughput pKJournal of computer-aided molecular design · 2021Article
- Ensembles Are Required to Handle Aleatoric and Parametric Uncertainty in Molecular Dynamics Simulation.Journal of chemical theory and computation · 2021Article
- Energy-entropy prediction of octanol-water logP of SAMPL7 N-acyl sulfonamide bioisosters.Journal of computer-aided molecular design · 2021Article
- Evaluation of log P, pKJournal of computer-aided molecular design · 2021Article
- 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
- AweGNN: Auto-parametrized weighted element-specific graph neural networks for molecules.Computers in biology and medicine · 2021Article
- Uncertainty quantification in classical molecular dynamics.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2021Article
- Quantum-mechanical property prediction of solvated drug molecules: what have we learned from a decade of SAMPL blind prediction challenges?Journal of computer-aided molecular design · 2021Article
- Determining the hydration free energies of selected small molecules with MP2 and local MP2 through adaptive force matching.The Journal of chemical physics · 2021Article
- SAMPL7 TrimerTrip host-guest binding affinities from extensive alchemical and end-point free energy calculations.Journal of computer-aided molecular design · 2021Article
- Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software.Journal of computer-aided molecular design · 2021Article
- SAMPL7 TrimerTrip host-guest binding poses and binding affinities from spherical-coordinates-biased simulations.Journal of computer-aided molecular design · 2021Article
- Semiclassical Vibrational Spectroscopy of Biological Molecules Using Force Fields.Journal of chemical theory and computation · 2020Article
- SAMPL6 host-guest binding affinities and binding poses from spherical-coordinates-biased simulations.Journal of computer-aided molecular design · 2020Article
24 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
Here, we give an overview of the small molecule hydration portion of the SAMPL4 challenge, which focused on predicting hydration free energies for a series of 47 small molecules. These gas-to-water transfer free energies have in the past proven a valuable test of a variety of computational methods and force fields. Here, in contrast to some previous SAMPL challenges, we find a relatively wide range of methods perform quite well on this test set, with RMS errors in the 1.2 kcal/mol range for several of the best performing methods. Top-performers included a quantum mechanical approach with continuum solvent models and functional group corrections, alchemical molecular dynamics simulations with a classical all-atom force field, and a single-conformation Poisson-Boltzmann approach. While 1.2 kcal/mol is still a significant error, experimental hydration free energies covered a range of nearly 20 kcal/mol, so methods typically showed substantial predictive power. Here, a substantial new focus was on evaluation of error estimates, as predicting when a computational prediction is reliable versus unreliable has considerable practical value. We found, however, that in many cases errors are substantially underestimated, and that typically little effort has been invested in estimating likely error. We believe this is an important area for further research.
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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.