Release 2.0 of the Dynamical Network Analysis Tutorial

Release 2.0 of the Dynamical Network Analysis Tutorial

This release contains updates to all tutorials to comply with API changes made to the Dynamical Network Analysis python package.
Extra text and explanations were introduced along the tutorials to helps integrate key concepts and tools.

Release 1.2 of the Dynamical Network Analysis Tutorial

Release 1.2 of the Dynamical Network Analysis Tutorial

This release contains updates to original tutorials and new tutorials that help users create node-groups for new residues, and prepare new CLI code for analysis and plotting in remote servers.

Start Here: Original tutorials (Interactive Jupyter notebooks) with a complete overview of the Dynamical Network Analysis pipeline for an enzyme and a ligand:

• Tutorial-Step_1-ProcessTrajectory.ipynb
• Tutorial-Step_2-AnalysisAndPlots.ipynb

Simplified tutorial for a single protein (no analysis of binding interfaces):

• Tutorial-Single-Protein-CLI-Step_1.py (Python script)
• Tutorial-Single-Protein-Step_2.ipynb (Interactive analysis with Jupyter notebook)

Stand-alone interactive Jupyter notebook to prepare for analysis with non-canonical residues:

• Tutorial-Non-Canonical-and-Non-Proteic-Residues.ipynb

CLI version of original tutorials for execution without a graphical interface in a remote server:

• Tutorial-Command-Line-Interface-Step_1.py
• Tutorial-Command-Line-Interface-Step_2.py

Release 1.1 of the Dynamical Network Analysis Tutorial

Release 1.1 of the Dynamical Network Analysis Tutorial

This release contains the material published along with the manuscript: Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics trajectories. J. Chem. Phys. (2020). DOI: 10.1063/5.0018980 .

Minor revisions were made, including version requirements for dependent python packages.