PandaMap: A Python Package for Comprehensive Visualization of Protein-Ligand Interaction Networks

Protein-ligand interaction diagrams are commonly used in structural and medicinal chemistry, but existing tools often force a difficult choice between comprehensive detection with tabular output, publication-quality figures requiring a paid license, or a complex scripting environment that assumes advanced expertise. PandaMap, a Python package, aims to simplify this process by providing a single command solution that generates a 2D interaction diagram, an interactive 3D viewer, a text report, a machine-readable CSV file, and a four-panel graphical summary.

The program reads PDB, mmCIF, and PDBQT files and detects 15 different types of interactions using crystallographically validated distance thresholds. It requires only standard libraries such as NumPy, Matplotlib, BioPython, and Requests, with RDKit enhancing the 2D ligand layout when available, although it is not a mandatory dependency.

The package pays special attention to hydrogen bonds, filtering them based on the true D-H-A angle when explicit hydrogens are present in the structure, matching the PLIP's 100 criterion, and relying solely on distance criteria otherwise. This approach ensures accurate measurement provenance is recorded for each interaction.

To demonstrate the package's effectiveness, the authors benchmarked PandaMap on three structurally diverse complexes: enolase with a phosphonate transition-state analogue (PDB 1ELS), the EGFR kinase in complex with erlotinib (1M17), and aldose reductase with IDD594 (1US0). The results show that PandaMap successfully recovers well-known contacts in these structures, such as the EGFR hinge hydrogen bond involving MET769 and the halogen bond between the bromine atom in IDD594 and THR113, both at distances matching those reported by PLIP.

The authors provide all detection thresholds, scoring weights, and the exact commands used for the interaction detection in the Supplementary Information. The package is released under the permissive MIT license, allowing for wide adoption and integration into various research workflows. PandaMap 4.3.0 is currently available on PyPI, the Python Package Index.