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DeepGraphLearning / GearNet

GearNet and Geometric Pretraining Methods for Protein Structure Representation Learning, ICLR'2023 (https://arxiv.org/abs/2203.06125)
MIT License
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Solution when alpha carbon coordinate is missing #46

Open YanjingLiLi opened 10 months ago

YanjingLiLi commented 10 months ago

Hi, since GearNet models each residue in the protein by the C_alpha coordinates, how do you handle the situation when the coordinate for alpha carbon is missing?

Oxer11 commented 10 months ago

The situation you says is quite uncommon. I assume that the alpha carbon is missing due to some data loss issues. In this case, we'd better discard the corresponding residues, or use some tools like pdbfixer to fix the pdb file.