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StructBioinfo/BioMD-AutomatedWorkflow

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App README

🧬 BioMD AutomatedWorkflow

Professional web platform for protein–ligand molecular dynamics analysis.

Features

⚡ Option 1 — Trajectory Analysis (instant)

—Upload XTC/TRR trajectory + GRO/PDB topology
—Get RMSD, RMSF, Radius of Gyration, Free Energy Landscape, P-L Distance plots
—Download all plots as ZIP + analysis report

🖥 Option 2 — Full MD Simulation (Pasteur HPC)

—Upload PDB + SDF/MOL2, fill contact form
—Request emailed to Institut Pasteur de Tunis HPC team
—Results (plots + report + ZIP) delivered by email

Local run

bash

git clone https://github.com/rihabmahjoub/BioMD_AutomatedWorkflow
cd BioMD_AutomatedWorkflow
pip install -r requirements.txt
uvicorn main:app --reload --port 7860
# Open http://localhost:7860

HF Space secrets (Settings → Variables and secrets)

Key	Value
`SMTP_HOST`	`smtp.gmail.com`
`SMTP_PORT`	`587`
`SMTP_USER`	Your Gmail address
`SMTP_PASS`	Gmail App Password
`ADMIN_EMAIL`	Lab email (Pasteur)

Citation

Mahjoub R., Mahjoub G., Khamessi O., Ghedira K.
BioMD_AutomatedWorkflow. Manouba University / Pasteur Institute of Tunis.
https://github.com/rihabmahjoub/BioMD_AutomatedWorkflow