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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.

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

This is to be done in two stages:

Stage 1: Pre-Processing of MD ensemble

This stage involves calculating descriptors of dynamics and pairwise interaction energies for all residue pairs (except self) from the MD ensemble:

1.1 Descriptors of dynamics and

1.2 Calculate Pairwise interaction energies

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Stage 2: DyNoPy analysis

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.

2.1 Coevolution analysis

2.2 Calculate Rho matrix

2.3 Calculate J matrix

2.4 Network analysis

2.5 Visualisation

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