TCRdock
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phbradley
python tools for TCR:peptide-MHC modeling and analysis
Hello, Apologies if I've misunderstood a crucial step in using the TCRdock tool. I have successfully generated a `pdb` file of a TCRpMHC complex and wish to compare it to...
It would be convenient if the output structure files from a modelling run had the supplied pLDDT values (in `.npy` form) contained within the PDB files. This would be consistent...
When running `run_prediction.py`, the output files get written to the current working directory. This is inconvenient as potentially a lot of output files are generated, and it may be desirable...
I have alphafold 2.3.2 installed and running using: python3 alphafold/docker/run_docker.py ... but I can't figure out how to run TCRdock's run_prediction.py "in the alphafold docker instance" Apologies for my lack...
When running the `python setup_for_alphafold.py` script, the alignment performed by `tcrdock.sequtil.blosum_align` involves the deprecated `Bio.SubsMat` module, triggering the following warning at the start of each run: ``` /home/cam/anaconda3/envs/tcrdock_test/lib/python3.8/site-packages/Bio/SubsMat/__init__.py:126: BiopythonDeprecationWarning: Bio.SubsMat...
Change `scorematrix` to use updated `Bio.Align.substitution_matrices` module to prevent deprecation warning #15 Note that the new `Bio.Align.substitution_matrices.Array` object has a `dict( ... )` wrapper before passing it to `pairwise2.align.globalds(...)` to...
I want to try tcrdock. conda env is installing well. But when I run examples, the errors are appeared. " No module ... tensorflow" when i fix the prob. then...
Hey Philip, Thanks a lot for creating this tool, I am currently looking into how I can best put it to use! I have a question related to the AF...
Hi Phil! Thank you so much for all the work into creating and curating this great resource! I've been interested in leveraging TCRdock for predicting TCR binding specificity for some...
Hello, The script that prepares the data for prediction, setup_for_alphafold.py, is long when you have a lot of data. I've noticed that it's not parallelized, is it possible to speed...
