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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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What is input (Tensor) – input node representations for GearNet #57

Open Heisenburger2020 opened 9 months ago

Heisenburger2020 commented 9 months ago

Dear Sir/Madam,

Thank you for your fantastic paper GearNet.

I wish to finetune Gearnet (distance prediction) for some other downstream tasks.

Now I have all atom positions and residue type and atom type. I used the same operation as fold3d to get protein. However, I do not know how can I get input (Tensor) – input node representations. I could not understand how those APIs passed this input into GearNet.

Yours Sincerely, Jiale Zhao

Oxer11 commented 9 months ago

Hi, thanks for the good words!

To use GearNet on your customized dataste, you can follow this tutorial, which describes how to use TorchDrug to construct data.Protein object and pass it into GearNet. Also, you can see this tutorial to learn about how to use pre-trained checkpoints.

Feel free to ask me if there are any other questions.