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facebookresearch / esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins
MIT License
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Contact prediction for multimeric proteins #678

Open AnjaliSetiya opened 2 months ago

AnjaliSetiya commented 2 months ago

Hi all I'm interested in generating contact maps from the ESM2 attention heads as described in the following github notebook: https://github.com/facebookresearch/esm/blob/main/examples/contact_prediction.ipynb. But it is not clear to me if I want to give hetero dimer or multimeric protein as FASTA for predicting contact maps how can I do that. How should the input be given for multi chains for contact map prediction.

AlejandroSanchezCano commented 2 months ago

Hi,

I am facing a similar problem. I want to generate ESM2 embeddings for dimeric proteins. Is appending the sequences a good idea? I have also modelled the 3D structure of these dimers with ESMFold. Could I use those structures to generate ESM2 embeddings?