openbabel
Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Schake, Bolz, et al. (2025), https://doi.org/10.1093/nar/gkaf361
Python script that receives a molecular dynamics or Monte Carlo trajectory and performs agglomerative clustering to classify similar structures.
Open Drug Discovery Toolkit
Convert DOK files to various chemical structure formats using Open Babel.
