I have many pdb files (amino sequences are alike).

And I would like to use these data for machine learning.

In my problem, amino sequences have same length, but the number of atoms is not different.

I would like to deal with these data not losing structural information and organize them for ML.

I found the article below.

Conference Paper Encoding protein structure with functions on graphs

If you know other methods for this problem, please teach me.

If possible, let me know programs (Python and R are best for me).

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