ArticleJournal of computer-aided molecular design2022
Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches.
Article in Journal of computer-aided molecular design, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- CHARMM-GUIJournal of chemical theory and computation · 2025Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Chemical accuracy for ligand-receptor binding Gibbs energies through multi-level SQM/QM calculations.Physical chemistry chemical physics : PCCP · 2024Article
- Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment.The Journal of chemical physics · 2024Article
- Free energies at QM accuracy from force fields via multimap targeted estimation.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Drug Design in the Exascale Era: A Perspective from Massively Parallel QM/MM Simulations.Journal of chemical information and modeling · 2023Review
- Exploring Routes to Enhance the Calculation of Free Energy Differences via Non-Equilibrium Work SQM/MM Switching Simulations Using Hybrid Charge Intermediates between MM and SQM Levels of Theory or Non-Linear Switching Schemes.Molecules (Basel, Switzerland) · 2023Article
- Modern semiempirical electronic structure methods and machine learning potentials for drug discovery: Conformers, tautomers, and protonation states.The Journal of chemical physics · 2023Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Accurately predicting free energy differences is essential in realizing the full potential of rational drug design. Unfortunately, high levels of accuracy often require computationally expensive QM/MM Hamiltonians. Fortuitously, the cost of employing QM/MM approaches in rigorous free energy simulation can be reduced through the use of the so-called "indirect" approach to QM/MM free energies, in which the need for QM/MM simulations is avoided via a QM/MM "correction" at the classical endpoints of interest. Herein, we focus on the computation of QM/MM binding free energies in the context of the SAMPL8 Drugs of Abuse host-guest challenge. Of the 5 QM/MM correction coupled with force-matching submissions, PM6-D3H4/MM ranked submission proved the best overall QM/MM entry, with an RMSE from experimental results of 2.43 kcal/mol (best in ranked submissions), a Pearson's correlation of 0.78 (second-best in ranked submissions), and a Kendall [Formula: see text] correlation of 0.52 (best in ranked submissions).
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