PyPDBcomplex : Protein-Protein Complex Analysis Toolkit

PyPDBcomplex is a comprehensive Python toolkit for analyzing protein structures, with a focus on antibody-antigen complexes. It provides easy-to-use functions for extracting detailed structural features, analyzing molecular interactions, and comparing multiple structures. Features Core Capabilities PDB Parsing: Robust parsing with support for altloc, HETATM, and complex structures Selection System: Intuitive syntax for selecting chains, residues, and atoms Contact Analysis: Detect H-bonds, salt bridges, hydrophobic contacts, pi-stacking, disulfides Interface Analysis: Identify interface residues and calculate buried surface area SASA Calculation: Solvent accessible surface area with bound/unbound comparison Geometry Analysis: Backbone angles (φ, ψ, ω), sidechain rotamers (χ), Ramachandran plots VdW Energy: Lennard-Jones energy decomposition Distance Analysis: Pairwise distances and distance matrices Advanced Features Residue Features: Comprehensive feature extraction combining all analyses Single Chain Analysis: Detailed characterization of individual protein chains Multi-Complex Comparison: Side-by-side comparison of multiple structures Hotspot Identification: Automatic identification of critical binding residues Interactive Visualizations: HTML dashboards with plotly Github repo for updates: https://github.com/fbabd/PyPdbComplex