Credits

The core functionality of MDPerTool is provided by OpenMM MD simulation software.

• MDPerTool was written in Python programming language (version 3.7). In addition to the Python core library, several open-source Python packages are used to provide the following functionality:

• PySide2 (a python wrapper around the Qt desktop application development environment, v5.13.2) is used for all GUI elements.

• Matplotlib (v3.4.2) is used to display two-dimensional line plots included in the “Analysis” interface.

• Pyqtgraph (v0.12.1) is used to display two-dimensional line plots included in the "Monitoring" interface.

• ProDy (v2.0.1) is used for PDB manipulations, atom selections and all other general geometric tasks related to protein structures.

• Mdtraj (v1.9.7) is used to convert trajectory file formats to OpenMM positions DCD for further processing using ProDy.

• PyMol by Schrödinger (open source version v2.5.0) is used as the embedded molecule viewer in the "Perturbation" and "Analysis" interfaces of MDPerTool.

• Numpy (v1.21.0) is used for all operations related to matrices, which occur throughout the computation workflow of MDPerTool.

• Pandas (v0.20.3) is used to store, process and save data throughout the computational workflow of MDPerTool.

• Networkx (v2.6) is used to construct Protein Residue based Networks and calculation of intersection and shortest paths.