I have about 2000 of proteins ligands from Protein Data Bank and a lot of their characteristics like full name, molecular formula, SMILES, etc. I would like to classify them in several broad groups according to their chemical features. Is there any database with such data?
Thank you!
Pavel V Pogodin
Hi, Kirill, I am not aware about such database, but there is a software suited for the task of chemical classification (see link to the original publication).
Also, you can simply cluster your set of compounds based on their chemical features.
Article ClassyFire: automated chemical classification with a compreh...
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Nikita Ivanisenko
Hi, Kirill! you can try fingerprints based clustering, e.g. RDkit for python can do this (http://www.rdkit.org/docs/Cookbook.html#clustering-molecules)
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