diff --git a/projects/PP2A-B55-design/README.md b/projects/PP2A-B55-design/README.md index 3b096af8dc5ab78701aa6f80907ca574e812eb74..d8db478f7e54f80c44d07a77994ec310e8ab83b9 100644 --- a/projects/PP2A-B55-design/README.md +++ b/projects/PP2A-B55-design/README.md @@ -10,14 +10,21 @@ _ 4 models directories : screen_256, holoenzyme, relaxes_figures and design - [NAME].json their respective scores for every model except the relaxed models containg the string 'only_pep' in their NAME Modelling setup: - - -Special features here: +- Classic ColabFold setup with PDB coordinates and scores JSON and link to UniProt +- Two custom model quality scores (ipLDDT, iPAE) +- Experimental validation of binding and only validated or known interactions exported to 3D-Beacons +- Four different modelling setups (PPI screening, relaxed models of selected screening results, full holoenzyme complex, design of protein-peptide complex) + +Special features here compared to PRC-complexes script: +- UniProt-link: deal with subsets of sequences and with old versions and fixed cache of UniProt data (keyed also on entity sequence) +- Use of modelcif.reference.SeqDif to deal with mismatches between UniProt and entity sequence +- Deal with synthetic constructs (design) which do not have a link to UniProt +- Custom cut of JSON scores for PAE and pLDDT for some relaxed models +- Updated _get_cf_config function to deal with null values in ColabFold's config.json and to reset tpl_db and tpl_db_version if no templates used Content: - translate2modelcif.py : script to do conversion (run in virtual environment with same setup as Docker container here but with OST 2.8 and very latest main branch of python-modelcif and python-ihm from 20.6.2024) - modelarchive_submission.zip: example inputs to convert selected complex from this set, compressed - expected_output_modelcif.zip: compressed output from running conversion of modelarchive_submission with the following command : - `python3 translate2modelcif.py ./modelarchive_submission ./modelcif --no-extra-files`