ColabDesign
ColabDesign copied to clipboard
sokrypton
Making Protein Design accessible to all via Google Colab!
Hi there! I found your colab coincidentally and wanted to try hallucinating some binders using it for the protein "8DYS" on PDB. However, when using the recommended settings and initializing...
Run the partial hallucination using the following code and got out of memory issue. the complex is composed of two chains ['A', 'C'], A chain has 1505 residues. Need to...
Implements FlashAttention similarly to https://github.com/google-deepmind/alphafold/pull/931 For a 759 residue protein and model_5 this improves runtime 2.2x on an L4 (37.3 $\rightarrow$ 16.9 seconds [with minibatching of 256 for non-flash attention...
run file: af/examples/peptide_binder_design.ipynb hope: the binder binds at the hotspot, e.g. 32-41 index in the target chain. results: the binder not binds at the hotspots at the target chain at...
Hello, I'm trying to setup a local colabdesing instance about AfDesign - binder + hotspot test, but I encounter this error "WARNING: 'model_1_ptm' not found WARNING: 'model_2_ptm' not found" while...
The [Fold Conditioning notebook ](https://colab.research.google.com/github/sokrypton/ColabDesign/blob/main/rf/examples/diffusion_foldcond.ipynb) seems to be broken, both in main and beta. I guess the diffusion fails for some reason and then the output can't be displayed. Just...
[2023_Cyclic peptide structure prediction and design using AlphaFold](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9980166/ ) mentions `"Example scripts for structure prediction, sequence design, and hallucination are available at https://github.com/sokrypton/ColabDesign/blob/main/af/examples/af_cyc_design.ipynb"` However, I can't see prediction of cyclic...
i am trying to run cyclic peptide using the notebook template provided in afdesign. However i get the following error when i run it: 2 af_model = mk_afdesign_model(protocol="fixbb", data_dir="../params/") 3...
Hi, Hope youre doing well. ColabFold gives users an a3m full of Uniprot and Uniparc identifiers, however in this build it doesnt get this and instead theyre changed to numbers....
Not sure I am getting this error, I don't seem to get it consistently either. But right now I am getting this error consistently. FileNotFoundError: [Errno 2] No such file...
