ArticleFrontiers in molecular biosciences2022
Assessing the effect of forcefield parameter sets on the accuracy of relative binding free energy calculations.
Article in Frontiers in molecular biosciences, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed.
- Unveiling molecular moieties through hierarchical Grad-CAM graph explainability.BMC bioinformatics · 2025Article
- Residence time in drug discovery: current insights and future perspectives.Pharmacological reports : PR · 2025Review
- Article
- Elucidating the molecular determinants for binding modes of a third-generation HIV-1 integrase strand transfer inhibitor: Importance of side chain and solvent reorganization.bioRxiv : the preprint server for biology · 2023Article
- Scaffold Hopping and Optimization of Small Molecule Soluble Adenyl Cyclase Inhibitors Led by Free Energy Perturbation.Journal of chemical information and modeling · 2023Article
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2 authors.
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Abstract
Software for accurate prediction of protein-ligand binding affinity can be a key enabling tool for small molecule drug discovery. Free energy perturbation (FEP) is a computational technique that can be used to compute binding affinity differences between molecules in a congeneric series. It has shown promise in reliably generating accurate predictions and is now widely used in the pharmaceutical industry. However, the high computational cost and use of commercial software, together with the technical challenges to setup, run, and analyze the simulations, limits the usage of FEP. Here, we use an automated FEP workflow which uses the open-source OpenMM package. To enable effective application of FEP, we compared the performance of different water models, partial charge assignments, and AMBER protein forcefields in eight benchmark test cases previously assembled for FEP validation studies.
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