Structural models and molecular dynamics data for cathepsin B, S, and K complexes with glycosaminoglycan-like ligands relevant to allosteric regulation

This repository contains structural models and molecular dynamics input files for complexes of cathepsins B, S, and K with three glycosaminoglycan-like ligands: naphthalene-1,3,6-trisulfonate (NTS), amide-linked bis(naphthalene disulfonate) (BNS), and suramin. Initial protein and ligand structures used for molecular docking are provided in AutoDock3 format. For each cathepsin–ligand complex, the three most populated docking clusters are included, with three representative binding poses per cluster. The repository further contains system topologies and initial coordinates for molecular dynamics simulations in AMBER format (.parm7 and .rst7), ligand library files required for tleap, molecular dynamics input files, and scripts used for post-processing and analysis of the MD trajectories.