ArticleJournal of chemical information and modeling2023
ChemFlow─From 2D Chemical Libraries to Protein-Ligand Binding Free Energies.
Article in Journal of chemical information and modeling, 2023. 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.
- DockM8: an all-in-one open-source platform for consensus virtual screening in drug design.Journal of cheminformatics · 2026Article
- EasyDock 1.3: An Automated Pipeline for Molecular Docking.Journal of chemical information and modeling · 2026Article
- Artificial Intelligence in Molecular Optimization: Current Paradigms and Future Frontiers.International journal of molecular sciences · 2025Review
- In silico discovery of alkaloids as VEGFR-2 inhibitors with favorable toxicity profiles: insights from molecular dynamics and MM/GBSA.In silico pharmacology · 2025Article
- StreaMD: the toolkit for high-throughput molecular dynamics simulations.Journal of cheminformatics · 2024Article
- In Silico Screening of 1,3,4-Thiadiazole Derivatives as Inhibitors of Vascular Endothelial Growth Factor Receptor-2 (VEGFR-2).Current issues in molecular biology · 2024Article
- ChemFlow_py: a flexible toolkit for docking and rescoring.Journal of computer-aided molecular design · 2023Article
- EasyDock: customizable and scalable docking tool.Journal of cheminformatics · 2023Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The accurate prediction of protein-ligand binding affinities is a fundamental problem for the rational design of new drug entities. Current computational approaches are either too expensive or inaccurate to be effectively used in virtual high-throughput screening campaigns. In addition, the most sophisticated methods, e.g., those based on configurational sampling by molecular dynamics, require significant pre- and postprocessing to provide a final ranking, which hinders straightforward applications by nonexpert users. We present a novel computational platform named ChemFlow to bridge the gap between 2D chemical libraries and estimated protein-ligand binding affinities. The software is designed to prepare a library of compounds provided in SMILES or SDF format, dock them into the protein binding site, and rescore the poses by simplified free energy calculations. Using a data set of 626 protein-ligand complexes and GPU computing, we demonstrate that ChemFlow provides relative binding free energies with an RMSE < 2 kcal/mol at a rate of 1000 ligands per day on a midsize computer cluster. The software is publicly available at https://github.com/IFMlab/ChemFlow.
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Registered trials
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.