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I am currently facing an issue with predicting protein-peptide complexes. I have successfully installed AlphaFold3 locally and received the model parameters. While I am able to predict individual prot…
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I greatly appreciate you providing the full training recipes for a protein language model, however our own test on a binding prediction task showed very poor performance of embeddings obtained from AM…
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Congratulations on Your Open Source Release!
I'm excited to see your work on "SLAM: structure-aware lysine β-hydroxybutyrylation prediction with protein language model" available as an open-source re…
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Notice tracel-ai from burn framework, this software must substitute to high performance predictions, like robotics, predict from data lake. Some molecular pretrained models use RoBERTa as base model, …
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Awesome work :)
I am thinking about finetuning this model on specific protein domain with MLM task.
As in, starting from the SaProt model weights, further finetuning on un-labeled dataset.
1. W…
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It looks like the script doesn't work when running on predictions that have modified residues. For example, running on a prediction that contains several Aceytyl-Lysine (three letter code "ALY") resid…
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Good afternoon,
I've been using the 3D NGL export to retrieve the cross-link distances and pseudobonds for provided homomer structures (AlphaFold predictions), in order to have, among all possible c…
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One protein (230 aa) plus ligand (phospholipid, ccdCodes = ["PCW"])
With one phospholipid, ligand structure is good and phospholipid (C18) found its way in the binding site with a reasonable orient…
smg3d updated
16 hours ago
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Hi,
Is there a way (or a flag) for having multiple PDB structures predicted for protein-protein complex with small molecule? The default is only one outout PDB given.
mtahe updated
7 months ago