Protein Modeling Scripts

A collection of Python scripts for protein structure analysis, homology modeling, and molecular dynamics simulations.

📁 Directory Structure

🧬 homology_modeling/

Scripts for protein homology modeling using MODELLER

• homology_modeller.py - Main homology modeling script with assessment
• hybrid_homology_modeller.py - Multi-template homology modeling
• mutation_modeller.py - Protein mutation modeling
• regional_hybrid_modeller.py - Region-specific hybrid modeling
• simple_modeller_disulfides.py - Basic modeling with disulfide bonds
• modeller_with_disulfides.py - Advanced disulfide constraint modeling
• model_comparison.py - Compare and assess protein models

🔍 structure_analysis/

Tools for protein structure analysis and modification

• structure_analyzer.py - General protein structure analysis
• analyze_cys_distances.py - Analyze cysteine distances for disulfide bonds
• add_disulfide_bonds.py - Add disulfide bond annotations to PDB files
• add_e2_disulfides.py - Add E2-specific disulfide bonds
• force_add_disulfides.py - Force add disulfide bonds regardless of distance

📊 pdb_processing/

PDB file downloading, processing, and extraction tools

• pdb-download.py - Download PDB files from RCSB
• pdb_sequence_extractor.py - Extract sequences from PDB files
• pdb_gap_analyzer.py - Analyze gaps and missing residues in PDB structures
• extract_e2_chains.py - Extract specific chains from PDB files (E2 protein focus)
• demo_pdb_extraction.py - Demo script for PDB chain extraction
• forced_substitution_aligner.py - Alignment with forced substitutions

🏃‍♂️ md_simulation/

Molecular dynamics simulation scripts

• simulate.folding.py - Protein folding simulations
• simulate.equilibrium.py - Equilibrium MD simulations

📂 temp_files/

Temporary files, model outputs, and intermediate results

• Generated PDB models
• MODELLER output files
• Alignment files (PIR format)
• Assessment results

🚀 Quick Start

Requirements

# Install dependencies
conda install -c conda-forge biopython
conda install -c salilab modeller
pip install requests numpy

Common Workflows

1. Basic Homology Modeling

cd homology_modeling/
python homology_modeller.py -p alignment.pir -t template.pdb -o output_dir

2. Add Disulfide Bonds to Models

cd structure_analysis/
python add_disulfide_bonds.py input_model.pdb output_with_disulfides.pdb

3. Download and Process PDB Files

cd pdb_processing/
python pdb-download.py 1ABC
python extract_e2_chains.py 1ABC.pdb

4. Analyze Protein Structures

cd structure_analysis/
python structure_analyzer.py protein.pdb
python analyze_cys_distances.py protein.pdb

📝 Usage Examples

Multi-template Homology Modeling

python homology_modeling/hybrid_homology_modeller.py \
  --alignment multi_template.pir \
  --templates template1.pdb template2.pdb \
  --output models/ \
  --num_models 5

E2 Protein Modeling Pipeline

# 1. Extract clean E2 chains
python pdb_processing/extract_e2_chains.py 8RJJ.pdb

# 2. Run homology modeling
python homology_modeling/simple_modeller_disulfides.py

# 3. Add disulfide bonds
python structure_analysis/add_e2_disulfides.py E2_model.pdb E2_final.pdb

🔧 Script Features

Homology Modeling

• ✅ Single and multi-template modeling
• ✅ Model quality assessment (DOPE, GA341, molpdf)
• ✅ Disulfide bond constraints
• ✅ Mutation modeling
• ✅ Loop refinement

Structure Analysis

• ✅ Disulfide bond detection and analysis
• ✅ Structure quality metrics
• ✅ Distance calculations
• ✅ Chain extraction and cleaning

PDB Processing

• ✅ Automated PDB downloading
• ✅ Sequence extraction
• ✅ Gap analysis
• ✅ Chain separation
• ✅ Structure cleaning

📚 Dependencies

• Python 3.7+
• BioPython
• MODELLER 10.7+
• NumPy
• Requests
• Math (built-in)

🤝 Contributing

1. Keep scripts focused and well-documented
2. Follow the directory structure
3. Include usage examples in docstrings
4. Test scripts before committing

📄 License

Academic and research use. Please cite appropriate software packages when publishing results.

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Organized structure for protein modeling workflows