deepbiologic
deepbiologic copied to clipboard
deepchem
Deep Learning Tools for Design of Biologic Therapeutics
https://www.nature.com/articles/s41598-017-04439-5 A cool paper that shows how a simple heuristic can find disease motifs in a dataset of B-cell receptor sequences drawn from (roughly) 50 healthy patients and 50 unhealthy...
Immunogenicity is one of the most serious problems facing the design of new biologics. In a nutshell, immunogenicity is when the patients immune system mounts a response against the introduced...
http://www.pnas.org/content/114/5/944.full Contains a large (by standards of field :-)) dataset of all antibodies tested in phase-2 or phase-3 clinical trials measured "criteria regarding the feasibility of their manufacture, stability in...
http://onlinelibrary.wiley.com/doi/10.1002/prot.24756/full Would be worth reimplementing, but looks like data uses proprietary dataset.
http://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/Welcome.php A useful overlay over PDB pulling out all antibody structures. Could be a useful source for building learning algorithms on antibodies.
Linking discussion from https://github.com/deepchem/deepchem/issues/616 Regular graph convolutions only draw in information from an atom's direct neighbors. Atrous graph convolutions could draw in information from an atom's bond-distance 2 or 3...