🧬 AutoDock Vina 1.2.7 — Streamlit Interface

A cloud-ready molecular docking workflow converted from the original Google Colab notebook.

Deploy to Streamlit Cloud

1. Push this folder to a GitHub repository
2. Go to share.streamlit.io and connect the repo
3. Set Main file path to app.py
4. Click Deploy — Streamlit Cloud handles all package installation automatically

Run Locally

# Install system dependencies (Ubuntu/Debian)
sudo apt-get install openbabel wget curl

# Install Python dependencies
pip install -r requirements.txt

# Launch the app
streamlit run app.py

Workflow (top to bottom)

Step	What it does
1 — Receptor	Download PDB from RCSB (or upload), auto-detect co-crystal ligand, set docking box, prepare PDBQT via OpenBabel
2 — Ligand	Enter SMILES, predict pKa, adjust protonation at target pH, generate 3D conformer, prepare PDBQT via Meeko
3 — Docking	Run AutoDock Vina 1.2.7 with configurable exhaustiveness and pose count
4 — Results	Score table, affinity bar chart, animated pose viewer, interactive pose selector, download buttons

Notes

• The Vina binary is downloaded at startup from the official GitHub release (~8 MB)
• OpenBabel is installed as a system package via packages.txt
• All intermediate files live in a temporary directory scoped to your session
• st.session_state preserves results between widget interactions — no need to re-run steps

Citations

AutoDock Vina 1.2:
Eberhardt, J.; Santos-Martins, D.; Tillack, A. F.; Forli, S.
J. Chem. Inf. Model. 2021, 61, 3891–3898. https://doi.org/10.1021/acs.jcim.1c00203

Meeko:
https://github.com/forlilab/Meeko

pKaPredict:
Hengphasatporn, K. et al. J. Chem. Inf. Model. 2026. https://doi.org/10.1021/acs.jcim.5c02852