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Welcome to the DyNoPy tutorial!

Hopefully, you will find the instructions provided here useful on how to use this tool.

If you have any questions please email Sarath Dantu or Alessandro Pandini.

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The final goal of DyNoPy is to generate the J-matrix and using network analysis extract the residue contributing to the functional dynamics.

Listed below are the sequence of steps on how to generate the J-matrix and extract the community of residues collectively contributing to the dynamics of interest.

This is to be done in two stages:

Pre-Processing

Step 0. Description of dynamics

Step 1. Coevolution analysis.

Step 2. Calculate Pairwise interaction energies

Step 3. Calculate Rho matrix

Step 4. Calculate J matrix

Step 5. Network analysis

Step 6. Visualisation

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General tips

You can invoke the help by using the -h flag. e.g.:

dyno_coevolution.py -h

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