DruGUI 2.0: Mapping Protein Druggability with Probe-Based Molecular Dynamics

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ID: 318563
2026
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Abstract
SUMMARY: We introduce DruGUI 2.0, a drug discovery tool for assessing the druggability of proteins, integrated into the ProDy application programming interface (API). DruGUI 2.0 is developed to facilitate the search for druggable sites while allowing for proteins' conformational flexibility. Simulations in explicit solvent, with an option to include membrane, are carried out in the presence of probe molecules selected from an expanded library of small molecules containing drug-like fragments. Druggable sites beyond orthosteric sites are identifiable, as well as the probes that show high affinity to bind to those sites. Characterization of the composition and position of the probes helps build pharmacophore models and estimate relative binding affinities. As a Python module with enhanced visualization features, DruGUI 2.0 complements, and benefits from, the vast collection of protein sequence, structure, and dynamics analyses modules accessible in ProDy. Case studies in the Supplemental Material showcase the utility of DruGUI 2.0 applied to both soluble targets and membrane proteins. AVAILABILITY: ProDy is open-sourced and freely available under MIT License from https://github.com/prody/ProDy. The code version of DruGUI 2.0 used for simulations is available on Zenodo : 10.5281/zenodo.20511357. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. TUTORIAL: http://www.bahargroup.org/prody/tutorials/drugui2_tutorial/index.html.
Reference Key
openalex_W7165751750 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Carlos Ventura, Ji Young Lee, Anthony T. Bogetti, Anupam Banerjee, Matthew Licht, I Bahar
Journal BMC Bioinformatics
Year 2026
DOI
10.1093/bioinformatics/btag429
URL
https://doi.org/10.1093/bioinformatics/btag429
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