Ligand-X Demo
Demo: Protein Structure Cleaning
Video Walkthrough
Coming Soon: Video walkthrough demonstrating protein cleaning in Ligand-X.
Data Flow Pipeline
When you submit a protein for cleaning, your data flows through these stages:
1. Structure Loading
- Fetch from RCSB PDB or parse uploaded file
- Identify chains, residues, and heteroatoms
2. Component Analysis
- Identify ligands, waters, ions, metals
- Classify each heteroatom group
3. Water/Ion Removal
- Remove crystallographic waters (optional)
- Remove buffer ions (optional)
4. Missing Residue Repair
- Identify missing residues from SEQRES
- Model missing loops using PDBFixer
5. Missing Atom Repair
- Add missing heavy atoms
- Rebuild incomplete sidechains
6. Hydrogen Addition
- Add hydrogens at physiological pH (7.4)
- Assign protonation states
Results
- Clean PDB file ready for simulation
- Report of modifications made
- Interactive 3D visualization (MolStar)
- Download options (PDB format)
Tools Used
| Stage | Tool | Purpose |
|---|---|---|
| Fetching | RCSB API | Download structures by PDB ID |
| Parsing | BioPython | Parse PDB format |
| Cleaning | PDBFixer | Comprehensive structure repair |
| Analysis | ComponentAnalyzer | Classify heteroatoms |
| Visualization | MolStar | Interactive 3D viewer |
Workflow Steps
- Input Structure: Enter a PDB ID (e.g., “1HSG”) or upload a PDB file
- Review Components: See identified ligands, waters, ions
- Select Options: Choose what to remove/keep
- Clean Structure: PDBFixer repairs and protonates
- Visualize: Inspect cleaned structure in MolStar
- Download: Export clean PDB for downstream analysis
Common Issues Fixed
| Problem | Solution |
|---|---|
| Missing residues | Loop modeling from sequence |
| Missing atoms | Sidechain reconstruction |
| No hydrogens | pH-dependent protonation |
| Alternate conformations | Select highest occupancy |
| Non-standard residues | Convert to standard or parameterize |