proteinfold
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nf-core
Protein 3D structure prediction pipeline
### Description of feature There are new DBs available both for Alphafold and Colabfold. We need to update the pointers to the new DBs and check that the pipeline still...
### Description of feature Add mention to the AWS Open Data Sponsorship Program in readme. Also update licenses in the s3 bucket and also check that everything is ready for...
### Description of the bug When running without `--alphafold2_db` (default) all of the DB paths are printed as `null/` in the Execution log on stdout. Looks like there is an...
### Description of the bug When you try and run an alphafold2 job (and presumably colabfold as well) using the conda profile, it always errors out with: `python3: can't open...
### Description of the bug The python code search.py cannot find uniref30_2202_db even though I already specified the path. Maybe I lost something important? Thanks a lot in advance. ERROR...
### Description of the bug Hi, We are trying to run the nfcore proteinfold pipeline in ec2. While running the alphafold, we are getting an error message saying HHblits failed....
## Changes This PR adds the [TCRdock](https://github.com/phbradley/TCRdock) tool as a mode option to proteinfold. It is a specialized version of AlphaFold focused on TCR:pMHC prediction. The integration into the pipeline...
### Description of feature Hey there! As part of my bachelors thesis, I am working on integrating TCR:pMHC structure prediction using the [TCRdock tool](https://github.com/phbradley/TCRdock) into the nf-core/proteinfold pipeline. This is...
### Description of feature Check that DBs provided/downloaded to the pipeline are not corrupted or partly missing to avoid downstream issues.
### Description of feature Integrate OpenFold into the nf-core/proteinfold pipeline. OpenFold is a faithful but trainable PyTorch reproduction of AlphaFold2. OpenFold has the following advantages over the reference implementation: -...
