ColabDesign
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sokrypton
Making Protein Design accessible to all via Google Colab!
Hello. This is somewhat related to #107 I am fixing the positions of some of the residues using the bias matrix as follows. ``` bias = np.zeros((af_model._binder_len,20)) fixpos = [1,11,15]...
i am pretty new in colab, i can't find the output sequence when finish the Model.design_3stage() run, can anyone help?thankyou! 
The rationale for doing this is to do AF2 prediction with a custom template. May I know if it is possible? Thank you!
Hi Thank you for your great work! I wonder if there are any way to see sequences that are generated during each run! I am running AFdesign in colab at...
Is it possible to get the predicted aligned error files (PAE.json) when running the RFdiffsuion notebook? Thanks a lot.
Would it be possible to allow the user to select the model Complex_beta_ckpt.pt in order to design binders that are not only helical?
Hi, the colab for RFdiffsuion is great, but I have many disconnections problems with the free google colab runtime. WOuld it be possible to translate the notebook to jupyter notebook...
In rf/utils.py, around line 78, should the 3 lines be added, in case the residue numbering in the original PDB file has a gap? Thanks! ``` if L > 0:...
With a toy example, my contig string is 'A 20 E 10' with a modified pdb structure. The output sequence is: TTCCPSIRSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN/RRRNNDKPVDMLYPMVAMEMTLGSEFEVME In the above output, the two target sequences...
Hi, Thanks for your efforts on ColabDesign. I noticed your new work on the preprint (https://www.biorxiv.org/content/10.1101/2023.05.09.540044v1). Do you have any plans to add this work to ColabDesign? Thanks.
