PatchProt checkpoint

[jlenzing]

Hi,

Is it possible to upload the pretrained PatchProt checkpoint? I only see pretrained ESM in the repo / Google Drive.

Thanks! :).

[Deagogishvili]

Hi,

Thanks for letting me know! Now uploaded patchprot/model_best.pth

Best,
D

[jlenzing]

@Deagogishvili Thanks for uploading the checkpoint weights!

When running PatchProt I hit RuntimeError: PytorchStreamer failed reading zip archive: failed finding central directory. I also hit this when trying to load the weights directly in PyTorch locally.

This suggests to me that the uploaded model weights are corrupted. Can you double check if this is the case? Otherwise try and upload the weights again.

Thanks a ton! :).

[xpan-bio]

Hi,你好

Thanks for letting me know! Now uploaded patchprot/model_best.pth谢谢你让我知道！现在上传了 patchprot/model_best.pth

Best,最好 D

Hello! I encountered the same issue mentioned in other comments. When loading the pre-trained model weights (model_best-001.pth), I get a "PytorchStreamReader failed reading zip archive: failed finding central directory" error. The file size appears normal (~2.87GB), but it seems the file might be corrupted or incomplete. Could you please help verify if the current model weights file is correct and complete? I've tried different PyTorch loading methods but none worked. Thank you so much for sharing this excellent work, and I'm really looking forward to trying out PatchProt once this issue is resolved!

[Deagogishvili]

Hi both,

Thanks to you both for checking. Apparently, the model weights got corrupted when I downloaded from the server. I have re-uploaded the one that also loads locally. If it still doesn’t work for you when you download it, I’ll try to split it into smaller chunks and upload them separately. By the way, if you have any suggestions on how to provide such large files, please let me know.

I've now re-uploaded a verified version that loads correctly on my local machine. Please try downloading it again and let me know if you still encounter issues. If problems persist, I'll split the file into smaller chunks for more reliable downloading.

Alternative recommendations while we resolve this:
If you're interested in hydrophobic patch prediction, I'd highly recommend trying our MolPatch tool: https://github.com/Deagogishvili/MolPatch

• Works with predicted structures from AlphaFold
• Can process experimentally resolved protein structures directly
• Calculates patches from 3D structure rather than sequence prediction
• We'll be publishing MolPatch as a separate paper soon

For secondary structure predictions specifically, NetSurfP-3.0 remains state-of-the-art and is readily available while we fix the PatchProt issues: https://services.healthtech.dtu.dk/services/NetSurfP-3.0/


Best,
Dea