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DeepGraphLearning / SiamDiff

Code for Pre-training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction (https://arxiv.org/abs/2301.12068)
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Question about the RES task #1

Open YanjingLiLi opened 1 year ago

YanjingLiLi commented 1 year ago

Hi, I have a question about the RES task. For each example, the subunit indices contain atoms and residues from different chains of the protein. Do you just treat them as a complete protein chain to predict the type of residue at the masked place?

Oxer11 commented 1 year ago

Yes. The RES task is defined as predicting masked residue types based on local structural enviroments. So we save the subunit indices for each sample in each protein and use it to extract the corresponding part for each sample. https://github.com/DeepGraphLearning/SiamDiff/blob/2bc9682fbdfde76b75a3cc419fe4ad6bb7a7d85b/siamdiff/dataset.py#L237-L263