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Protein-Ligand Docking and Molecular Dynamics Twin

Open protein-ligand structure preparation, docking and MD workflow design, contact analysis, uncertainty, and validation. This application-facing research twin provides runnable local baselines, strict data and evidence contracts, and protected routes to higher-fidelity remote computation.

Installation | Quick start | Scientific status | Documentation | License

What version 0.2.0 provides

• Importable Python package and deterministic baseline.
• Executed notebook with printed scientific checks and a visual.
• Input validation, tests, provenance, agent rules, and compute preparation.
• Application-specific geometry or molecular structure artifacts.

v0.2.0 crystallographic flow

Run python scripts/run_contact_flow.py to audit MK1 contacts in open structure 1HSG. See docs/literature-evidence.md.

Scientific status

This is a Level 0 executable research baseline. Remote requests are prepared but not submitted. No production, safety, clinical, or universal predictive claim is made.

Installation

git clone https://github.com/vicena-labs/protein-ligand-docking-molecular-dynamics-twin.git
cd protein-ligand-docking-molecular-dynamics-twin
pip install -e .[dev]

Quick start

python scripts/run_baseline.py
pytest -q

License

Repository-authored code is MIT licensed. Third-party structures retain source attribution.