Trastuzumab-scFv CDR+FW Optimization Variants Iter0 x HER-2 (YM_0990)
Overview
YM_0990 are Trastuzumab designs against HER2. We explored several model hypothesis: (i) Does pre-training aid predicitivity and (ii) does the featurization of the input sequences matter. To test pretraining, we refer to mata_descriptions with the term warm to include pretraining, and cold to start from a randomly initialized seed. For featurization, we explored label-encoded sequences with a one-hot-encoder of amino acid identities, versus an ESM-featurized embedding to represent each sequence in the PPI.
Experimental details
We studied the efficacy of generating binders with different model hyperparameters. This dataset includes 20828 unique VHHs and 1 unique sequences. In this experiment, we enable designs to span a window that encompasses the frameworks and CDR regions.
A more extensive methods section can be found in our publication here.
Misc dataset details
We define the following binders:
A-library (scFvs)
There are several terms you can filter by:
TrastuzumabCDR_WT_<i>: These are WT replicates.TrastuzumabCDR_label_encoded_cold: Label encoded sequences with no pretrainingTrastuzumabCDR_label_encoded_warm: Label encoded sequences with pretrainingTrastuzumabCDR_esm_cold: ESM featurized sequences with no pretrainingTrastuzumabCDR_esm_warm: ESM featurized sequences with pretraining
Alpha-library
There is only 1 target of interest.