🧬 AbMelt: Enhanced Molecular Dynamics Pipeline
Predict antibody thermostability through multi-temperature molecular dynamics simulations
This enhanced space implements the complete AbMelt protocol with advanced visualizations:
- Structure generation with ImmuneBuilder and 3D visualization
- Multi-temperature MD simulations with trajectory analysis
- Comprehensive descriptor calculation and plotting
- Machine learning predictions with uncertainty quantification
- Interactive visualization of results
⚠️ Note: Full pipeline takes 2-4 hours per antibody due to MD simulation requirements.
Input Sequences
Simulation Parameters
Create 3D structure viewer and analysis plots
Pipeline Progress
Estimated Time
📊 Results
Thermostability Predictions
Pipeline Logs
📈 Visualization
📁 Download Results
🔬 3D Structure Viewer
📊 Analysis Plots
Upload Pre-calculated Descriptors
If you have already calculated MD descriptors, upload them here for quick predictions.
How to Use AbMelt
1. Input Requirements
- Heavy Chain: Variable region sequence (VH) of your antibody
- Light Chain: Variable region sequence (VL) of your antibody
- Simulation Time: 10-100 ns (longer = more accurate but slower)
- Temperatures: Comma-separated list (default: 300,350,400 K)
2. Pipeline Steps
- Structure Generation: Uses ImmuneBuilder to create 3D structure
- System Preparation: Sets up GROMACS molecular dynamics system
- MD Simulations: Runs simulations at specified temperatures
- Descriptor Calculation: Extracts molecular features from trajectories
- ML Prediction: Uses trained models to predict thermostability
3. Output Interpretation
- Tagg: Aggregation onset temperature - higher is better
- Tm,on: On-pathway melting temperature - thermal stability indicator
- Tm: Overall melting temperature - global stability measure
4. Tips for Best Results
- Use complete variable regions (110-130 residues typical)
- Longer simulations provide more reliable predictions
- Check logs for any warnings or errors
- Download trajectories for further analysis
Additional Resources
Frequently Asked Questions
Q: How long does the full pipeline take? A: Approximately 15-20 minutes per nanosecond per temperature. For 10ns at 3 temperatures, expect 2-3 hours. For 100ns simulations, expect 20-30 hours.
Q: Can I use this for nanobodies or single-domain antibodies? A: Yes, but you'll need to provide both VH and VL sequences. For nanobodies, you can duplicate the VH sequence as VL, though predictions may be less accurate.
Q: What if I only have the full antibody sequence? A: You need to extract just the variable regions (VH and VL). Use IMGT/V-QUEST or similar tools to identify variable region boundaries.
Q: Why are my predictions very low/high? A: Check that:
- Sequences are correct variable regions
- No unusual amino acids or modifications
- Proper sequence length (typically 110-130 residues)
Q: Can I compare multiple antibodies? A: Currently, process one at a time. Save results for comparison. Batch processing may be added in future versions.
Q: What does "GROMACS error" mean? A: Usually indicates:
- Severely malformed structure
- System preparation issues
- Memory constraints Try reducing simulation time or contact support.
Q: How accurate are the predictions? A: Based on published validation:
- Tagg: R² = 0.57 ± 0.11
- Tm,on: R² = 0.56 ± 0.01
- Tm: R² = 0.60 ± 0.06
Q: Can I use the trajectories for other analyses? A: Yes! Download the trajectory files and use with VMD, PyMOL, or other MD analysis tools.
| Heavy Chain Variable Region | Light Chain Variable Region |
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