Research data and workflows for the Geneva (Geneva-MM) project at Chopra Lab, focused on small‑molecule docking, compound–protein interaction analyses, and molecular dynamics (MD) simulations. The repository includes code and data to take ligands from interaction‑matrix style resources through docking and MD refinement, with utilities for aggregating results into downstream analysis tables.
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├── CANDO_interactions/ # Scripts/data to process CANDO interaction matrices
├── compound_protein_interaction/ # CPI model used for mapping compounds to protein targets
├── docking/ # CANDOCK Docking inputs, parametrization helpers, and result collectors
├── md_simulations/ # GROMACS-ready systems, trajectories, and MD analysis notebooks
├── .gitmodules # Submodules used in this repository (initialize after cloning)
└── .gitignore
If this repository contributes to your research, please cite the Chopra Lab and any associated publications from the Geneva project. (Add DOIs here once available.)
- Prageeth Wijewardhane (@gwijewar / @prageethrw)
- Matthew Muhoberac (@mmuhoberac)