drug-trajectory-analysis

What problem does it solve?

This Skill turns a protein–ligand molecular dynamics (MD) trajectory into quantitative binding-mode descriptors so you can judge pose stability and interaction quality without manual frame-by-frame inspection.

Core Features & Use Cases

• Ligand pose stability metrics: computes ligand heavy-atom RMSD and ligand center-of-mass (COM) drift over time.
• Binding-pocket dynamics: estimates pocket residue RMSF to identify flexible contact regions.
• Interaction quality over time: detects protein–ligand hydrogen bonds, computes residue contact occupancy, and optionally generates protein–ligand interaction fingerprints (IFPs) using ProLIF.
• Reproducible outputs for decision-making: writes CSVs and a JSON summary suitable for comparing refinement runs and go/no-go assessment.

Quick Start

Run trajectory analysis for ligand residue UNL by executing the command below to produce RMSD, COM drift, RMSF, hydrogen bonds, contacts, optional IFPs, and plots in your specified output directory. python .agents/skills/drug-trajectory-analysis/scripts/analyze_trajectory.py --topology md/system/complex_solvated.pdb --trajectory md/run/production.dcd --ligand_resname UNL --pocket_cutoff 5.0 --output_dir md/analysis/