Modelling of African Swine Fever proteome from USDA

Link to project in ModelArchive (incl. background on project itself)

Setup:

• Using AlphaFold for monomer predictions with default CASP14 setup (no PAE, no pTM, templates used and relaxation enabled)
  • 196 models done with default setup, 1 model (QP509L) with done with AF colab notebook and separate GROMACS relaxation step
• Input from them:
  • PDB files for top ranked relaxed model
  • CSV file with crosslinks (UniProt and NCBI), title, description and original filename

Special features here:

• Somewhat generic code for AlphaFold modeling step and sequence DBs used (can distinguish full_dbs and reduced_dbs and template search)
• pLDDT extracted from b-factors (simplest setup since no other QA scores anyway)
• Model file names did not contain information on AlphaFold model number (hence info in CSV file)
• Crosslinks to UniProt and NCBI (with sanity checks on both)
• Dealing with entries which cover subset of reference sequence (CP2475L.. for UniProt A0A2X0THU5)
• Special case (QP509L) with GROMACS model relaxation step (pLDDT fetched from separate file)

Content:

• translate2modelcif.py : script to do conversion based on CoFFE-sponge-proteins project (identical Docker setup used)