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Svensson-Lab / AlphaLigand

Code for Rapid and accurate deorphanization of ligand-receptor pairs using AlphaFold
https://www.biorxiv.org/content/10.1101/2023.03.16.531341v1
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The project is difficult to use #2

Open Luofan-KK opened 1 year ago

Luofan-KK commented 1 year ago

This is an interesting project with great potential for solving ligand-receptor pairing. However, I have encountered several issues that make it difficult for those who are not familiar with your code to use it effectively. Here are the problems I found:

  1. There is a merge conflict in the compute_msa_parallel.sh file, specifically in lines 15-20. Please resolve this conflict.
  2. In the run_parafold_no_template.sh script, you are passing the --data_dir argument to alphafold_script. However, it seems that ParallelFold/run_alphafold.py is unable to parse this argument correctly.
  3. The ParallelFold/run_alphafold.py script requires the --parameter_pat argument, which is not being passed by run_parafold_no_template.sh.

I hope these suggestions help in resolving the issues.

denizkavi commented 1 year ago

Thank you for bringing this to our attention, I'll get to resolve them right away. Thank you for your interest!