ginnm / deprot

Code for DeProt. A protein language model with quantizied structure and disentangled attention

• Move to https://github.com/ai4protein/ProSST.

deprot's Issues

Speed of quantization?

Hi,

First of all, thanks for the paper and for sharing the code - it seems like a novel and effective approach for discretizing structural elements. The zero shot performance on ProteinGym is impressive!

I am running into speed issues when I run the PDB quantizer. For now, it seems very slow when quantizing large structures. Would it be possible to move parts of the quantization step to GPU/CUDA to speed up?

Script for representation

Are there any scripts available to get representations/embeddings for a given sequence/structure?