Philip Bradley

Hi there, I'm also encountering the "Error" problem through the webgui with a single database file of ~600M. I have tried using the command line script provided here (https://github.com/jhpoelen/zenodo-upload) but...

Hi Paul, I bet that would be possible. For me, the bottleneck is running the predictions, so I haven't put much thought into doing that yet. Believe it or not,...

Also, note that there is an updated docking protocol and associated fine-tuned parameter set available. You can see an example of how that works in the google-colab jupyter notebook: https://github.com/phbradley/TCRdock/blob/main/tcrdock_colab_pipeline_v1.ipynb

tldr: 1. update to the newest version of the TCRdock repository 2. add the flag `--new_docking` when running `setup_for_alphafold.py` 3. add the flags `--model_names model_2_ptm_ft4 --model_params_files /path/to/tcrpmhc_run4_af_mhc_params_891.pkl` when running `run_prediction.py`,...

Good question! The new model just runs a single alphafold simulation per target, rather than running 3 and taking the best score by pMHC:TCR PAE, so in that sense it...

Hi there, Thanks for trying conga! It looks like there's an "unrecognized" TCR gene name. That could mean that there's a mismatch between the "TCR" (or BCR) type and the...

Hi there, Thanks for trying the code! Yes, there are some compatibility issues with alphafold and jax. Have you tried using an older version of jax, for example, 0.2.22, and...

Hi Guillem, Can you provide an example of the format of your input files? Do you have gene expression data or is this just TCR sequences? Take care, Phil ________________________________...

Hi Guillem, One more follow-up question: how many TCRs are you looking to analyze? Three other tools that might be more appropriate for single-chain data are * ALICE (Walczak lab)...

Yes! Oh, I just now realized that this was not a "conga" question but a "tcrdist" question. Sorry, Guillem, I have been getting many github emails about a different software...