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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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How to download and preprocess the PDB experimentally-determined protein. #22

Closed Dreamer312 closed 1 year ago

Dreamer312 commented 1 year ago

"Specifically, we extract 123,505 experimentally-determined protein structures from PDB"

Hi, appreciate your great work! I am quite new in this area. Could you please tell me where is the code to download and preprocess those experimentally-determined proteins?

ChrisAllenMing commented 1 year ago

Hi, thanks for your interest in our work. In our project, we use the list of high-quality pdb files from this website (e.g., with resolution higher than 2.5 angstrom) in the dataset ablation experiments. However, since we did not observe performance gain by using these experimental structures, we did not pay more efforts on releasing these data.

Dreamer312 commented 1 year ago

Thanks!