README.md

metadata

title: AbMelt Complete MD Pipeline
emoji: 🧬
colorFrom: blue
colorTo: purple
sdk: gradio
sdk_version: 5.46.1
app_file: app.py
pinned: false

AbMelt: Complete Molecular Dynamics Pipeline for Antibody Thermostability Prediction

This Hugging Face Space implements the complete AbMelt protocol for predicting antibody thermostability through multi-temperature molecular dynamics simulations.

Features

• Complete MD Pipeline: From sequence to thermostability predictions
• Structure Generation: ImmuneBuilder for Fv structure prediction
• Multi-temperature Simulations: 300K, 350K, 400K molecular dynamics
• Comprehensive Analysis: GROMACS + MDAnalysis descriptor calculations
• ML Predictions: Random Forest models for Tagg, Tm,on, and Tm

Quick Start

Local Testing

# 1. Validate the pipeline
python run_local.py test

# 2. View example sequences
python run_local.py examples

# 3. Start the web interface
python run_local.py run

Docker Usage

# Build and run with Docker
docker build -t abmelt-pipeline .
docker run -p 7860:7860 abmelt-pipeline

Open your browser to http://localhost:7860

Usage

1. Input heavy and light chain variable region sequences
2. Configure simulation parameters (start with 10ns for testing)
3. Wait for complete MD simulation pipeline (30 minutes to 4+ hours)
4. Download thermostability predictions and intermediate files

Example Sequences

Use these for testing:

Quick Test (Short sequences for 10ns runs):

• Heavy: QVQLVQSGAEVKKPGASVKVSCKASGYTFTSYYMHWVRQAPGQGLEWMGIINPSGGSTNYAQKFQGRVTMTRDTSASTAYMELSSLRSEDTAVYYCAR
• Light: DIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYST

File Structure

AbMelt_HF_Space/
├── app.py                    # Main Gradio application
├── run_local.py             # Local testing script
├── test_pipeline.py         # Validation tests
├── src/                     # Pipeline modules
├── mdp_templates/           # GROMACS simulation templates
├── models/                  # Pre-trained ML models
└── data/                    # Example data and sequences

Requirements

• System: GROMACS, Python 3.8+, 8GB+ RAM
• Time: 30 minutes (10ns) to 4+ hours (100ns)
• Hardware: CPU with 4+ cores recommended

Note

This Space runs complete molecular dynamics simulations. Due to computational requirements, simulations may take several hours to complete.