Protein-Ligand Binding Analysis with PLIP

Analyze protein-ligand interactions in PDB structures, generate comprehensive interaction reports, and create 3D visualizations.

When to Use

• Analyzing binding modes from crystal structures or docking results
• Identifying key interactions driving binding affinity
• Comparing ligand binding patterns across multiple structures
• Generating publication-ready interaction visualizations

Workflow

Step 1: Load PDB and Identify Ligands

from plip.structure.preparation import PDBComplex

complex = PDBComplex()
complex.load_pdb(pdb_file)

# Filter ligands by molecular weight (exclude ions/cofactors, MW > 150 Da)
ligands = []
for lig in complex.ligands:
    if lig.mol.molwt > 150:  # OpenBabel molecule object
        ligands.append(lig)
        complex.characterize_complex(lig)

Step 2: Analyze Interactions

from plip.exchange.report import BindingSiteReport

complex.analyze()

for key, interactions in complex.interaction_sets.items():
    report = BindingSiteReport(interactions)
    report_lines = report.generate_txt()
    # Parse interaction data from report_lines

Step 3: Generate Visualizations

from plip.basic.remote import VisualizerData
from plip.visualization.visualize import visualize_in_pymol
from plip.basic import config

config.PICS = True
config.OUTPATH = output_dir
config.BACKGROUND = "white"
config.CARTOON = True

for key in complex.interaction_sets:
    data = VisualizerData(complex, key)
    visualize_in_pymol(data)

Expected Outputs

Interaction Types Reported

Score Interpretation

• More H-bonds: Generally indicates stronger, more specific binding
• Hydrophobic contacts: Contribute to binding entropy
• Water bridges: Can enhance or reduce binding affinity
• π-stacking: Important for aromatic ligand recognition

Error Handling

Dependencies

pip install plip pymol-open-source

Example Usage

# Analyze EGFR-erlotinib complex (1M17)
python examples/basic_example.py --pdb tmp/pdb_1m17.pdb --output ./results/

See examples/basic_example.py for complete implementation and references/advanced.md for batch processing workflows.