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tests
README.md
translate2modelcif.py
README.md

Modelling of Spongilla lacustris proteome with functional annotations

Main links:

Setup:

  • Using ColabFold for monomer predictions with AlphaFold without links to sequence databases
  • Input from them:
    • one tarball for the PDB files
    • one tarball for the JSON files
    • a CSV file with title and description for each protein
    • FASTA file with all sequences (used for sanity checks)

Special features here:

  • Description is long multiline text which includes output from functional annotation
  • First set of models converted by us to ModelCIF
  • Includes generic code for handling of ColabFold setup based on config.json
  • Includes test code for conversion of ModelCIF to content displayed in ModelArchive

Content:

  • translate2modelcif.py : script to do conversion; compatible with Docker setup from ma-wilkins-import (and script based on code there)
  • tests folder with
    • custom Docker setup used locally (Mac; with extra libraries for testing) and on work machine (managed CentOS with old docker version)
    • test_modelCIF_MA.py to convert ModelCIF to content displayed in ModelArchive (needs gemmi library)
    • test.ipynb and .html for tests performed during development