Merge branch 'PP2A-B55-design'

projects/PP2A-B55-design/README.md

+# Modelling of PP2A-B55-design
+
+[Link to project in ModelArchive](https://www.modelarchive.org/doi/10.5452/ma-osf-ppp2r2a) (incl. background on project itself)
+
+Input files for conversion:
+- info_of_submitted_structures.csv with metadata (incl. per chain mapping to entity description, subsetting, UniProtKB AC, iPlddt and iPAE scores, binding experiment results )
+_ 4 models directories : screen_256, holoenzyme, relaxes_figures and design
+- config.json in every directory above
+- [NAME].pdb for each model NAME listed in info_of_submitted_structures.csv, in the directory indicated in the metadata
+- [NAME].json their respective scores for every model except the relaxed models containg the string 'only_pep' in their NAME
+
+Modelling setup:
+- 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`
+