ArticleJournal of computer-aided molecular design2018
An explicit-solvent hybrid QM and MM approach for predicting pKa of small molecules in SAMPL6 challenge.
Article in Journal of computer-aided molecular design, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Digitized dataset of aqueous acid dissociation constants.RSC advances · 2026Article
- pKa prediction for small molecules: an overview of experimental, quantum, and machine learning-based approaches.Journal of computer-aided molecular design · 2025Review
- Dataset for quantum-mechanical exploration of conformers and solvent effects in large drug-like molecules.Scientific data · 2024Article
- Calculating the Aqueous pKAntioxidants (Basel, Switzerland) · 2023Article
- Insights into the coordination chemistry of antineoplastic doxorubicin with 3d-transition metal ions ZnJournal of computer-aided molecular design · 2023Article
- Improving Small Molecule pKFrontiers in chemistry · 2022Article
- 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
- Overview of the SAMPL6 pKJournal of computer-aided molecular design · 2021Article
- Multi-phase Boltzmann weighting: accounting for local inhomogeneity in molecular simulations of water-octanol partition coefficients in the SAMPL6 challenge.Journal of computer-aided molecular design · 2020Article
- Standard state free energies, not pKJournal of computer-aided molecular design · 2020Article
- A deep learning approach for the blind logP prediction in SAMPL6 challenge.Journal of computer-aided molecular design · 2020Article
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Authors and funding
4 authors.
Funding
Abstract
In this work we have developed a hybrid QM and MM approach to predict pKa of small drug-like molecules in explicit solvent. The gas phase free energy of deprotonation is calculated using the M06-2X density functional theory level with Pople basis sets. The solvation free energy difference of the acid and its conjugate base is calculated at MD level using thermodynamic integration. We applied this method to the 24 drug-like molecules in the SAMPL6 blind pKa prediction challenge. We achieved an overall RMSE of 2.4 pKa units in our prediction. Our results show that further optimization of the protocol needs to be done before this method can be used as an alternative approach to the well established approaches of a full quantum level or empirical pKa prediction methods.
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