Getting Started with CCMgen and CCMpredPy

This section provides basic tutorials of typical use cases of CCMpredPy and CCMgen. You can find some example data and output generated by both tools in the examples directory of the repository.

Preparing Data

Find an example alignment taken from the PSICOV supplementary data in examples/1atzA.fas. In general, you can run CCMpredPy on any FASTA-formatted multiple sequence alignment although results will be better the more sequences you have per column in the alignment.

Copy over examples/1atzA.fas and examples/1atzA.pdb to a new directory data/ which will be our working directory.

Tutorials

1. Compute and Visualize Contact Maps
2. Learn Accurate Models with Persistent Contrastive Divergence
3. Generate Realistic Protein Alignments

Conclusion

Getting started learning MRF models from alignments of protein families with CCMgenPy and sampling sequences with CCMgen is straightforward but there are many more options available to fine-tune the learning and sequence generation. See the CCMgen and CCMpredPy documentation for more information.