EvoProtGrad
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NREL
Directed evolution of proteins in sequence space with gradients
I was just wondering is it possible to get the importance score of the protein sequence using EvoProtGrad model? For instance, in https://huggingface.co/datasets/waylandy/phosformer_curated data there are kinase enzymes. Now I...
Hi, Is it possible to get the weight of a protein sequence using EvoProtGrad?
In the paper [Language models enable zero-shot prediction of the effects of mutations on protein function](https://www.biorxiv.org/content/10.1101/2021.07.09.450648v2) the ESM folks introduce the "Masked Marginal Scoring" method to compute effects of mutations...
When using EvoProtGrad with a large number of parallel chains and/or a large pLM, emptying the GPU cache and garbage collection appear to help with OOM issues. For example, adding...
Hi, This is a great paper and I was wondering whether it is possible to extend this approach of directed evolution to antibodies as well. For instance, I was thinking...
Identified issues and corrected them that led to sequences not matching the scores the sampler returned, as well as sequences being accepted despite accepted being false as a side effect...
I identified and fixed several bugs in the sampler.py file which resulted in: 1. Accepting proposed sequences even when accepted is False. 2. Lost alignment between the sequences in the...
Hi, thanks for the great work! I was working with some evaluation models that use ProtT5 and Ankh PLMs, and these models do not have a token; they only have...
