ColabDesign
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sokrypton
Making Protein Design accessible to all via Google Colab!
I am trying to upload the PDB (link: https://www.dropbox.com/s/koxlbk5ntgzzlv6/protchain1.pdb?dl=0) which only has chain A in the RF Diffusion Colab but I am getting the following error: ``` 7ki0.pdb(chemical/x-pdb) - 264951...
Hi everybody, did someone experience issues with AfDesign concerning the size limit (number of amino acid residues) of the target used to design the cyclic peptide binder? Namely, in my...
I am interested in using RFdiffusion to redesign a signaling protein that is a dimer. I want to use the binding motif from each protein in the dimer and symmetrically...
- added iPTM calculation - in predict.ipynb, the download links currently point to gezmi/Colabdesign, this needs to be corrected after merge.
When template mode is set to custom and PDB_ID and chain_ID are defined, the code fails to retrieve the pdb. This presumably has something to do with the module that...
Hi there, I wonder if you would also implement the ca-only mode in ProteinMPNN ? That would be a great help.
For the soft or logit design phase, how is the aatype information passed to AF2 structure module? I believe that part needs discrete amino-acid identities in order to assign frames...
I was wondering if there is currently a way to generate homo-oligomeric binders for homo-oligomeric targets? When I try something like this, where i supply a binder scaffold: ``` af_model...
Hiya, When installing colabdesign from Git (`pip3 install git+https://github.com/sokrypton/ColabDesign.git`) the following deprecation warning shows up: `DEPRECATION: Building 'colabdesign' using the legacy setup.py bdist_wheel mechanism, which will be removed in a...
Is there a way to use the CA-only ProteinMPNN models?
