DynaPIN Application Examples

DynaPIN Test Cases This repository contains the Molecular Dynamics (MD) trajectories and validation data for the DynaPIN. It includes inputs and analysis outputs for an extended validation dataset of 12 protein complexes derived from Docking Benchmark v5.5, evenly spanning rigid, medium, and difficult targets. Directory Overview: Trajectory_Inputs/: Raw trajectory (.dcd) and topology (.pdb) files of test cases required to run the tool. DynaPIN_Outputs/: Pre-computed results organized into visualization figures, numerical tables (CSV data for metrics and properties), and processed structure files for each test case. Usage: Please refer to the DynaPIN GitHub Page for installation instructions. An example reproduction command is given below: dynapin --output_dir=6CWG_dynapin --trajectory_file=6CWG/production1.dcd --commands=all_analysis,all_plots --topology_file=6CWG/6CWG_input.pdb --stride=5 --foldx_path=your_foldx_path/