Work

DynaPIN Application Examples

Year: 2026

Type: dataset

Abstract: DynaPIN Test Cases This repository contains the Molecular Dynamics (MD) trajectories and validation data for the DynaPIN. It includes inputs and analysis outputs for three diverse protein complexes (6CWG, 1ZM4, 2OT3) derived from Docking Benchmark v5.5. 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/

Source: Zenodo (CERN European Organization for Nuclear Research)

DOI: 10.5281/zenodo.18331984

Authors: Barlas, Ayşe Berçin, Özsan, Atakan, Chantal, Prévost, Sacquin-Mora, Sophie, Karaca, Ezgi

Institutions: Izmir Biomedicine and Genome Center, Centre National de la Recherche Scientifique

Language: English

Topic: Protein Structure and Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

OpenAlex ID: W7125369031

Cites:

Cited by:

Related to: 10