Tutorials

Notebooks

These tutorials aim to provide a comprehensive set of functions for analysis/visualizations. If you are new to ProDy packages, we suggest you to start with these notebooks to obtain a comprehensive overview of different functions and analyses.

• Getting started - ProDy basics
• Gaussian Network Model (GNM): comprehensive
• Anisotropic Network Model (ANM): comprehensive
• Essential Site Scanning Analysis (ESSA): comprehensive

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Python codes

These python scripts aim to provide a quick start for your specific purpose. For example, you may want to perform Gaussian Network Model analysis and visualize the mode profiles or generate a color-coded protein figure based on the size and direction of motions. These tutorials mean to prepare users with the minimal lines of codes required to perform the analysis and conveniently plot relevant results without going through all the logistics. If you need more explanations/information, please refer to the notebooks listed above and the ProDy website (http://www.bahargroup.org/prody/).

• Gaussian Network Model (GNM): quick start
• Anisotropic Network Model (ANM): quick start
• Essential Site Scanning Analysis (ESSA): quick start