{"id":26713,"library":"alphafold-colabfold","title":"AlphaFold ColabFold","description":"An implementation of the inference pipeline of AlphaFold v2.3.1, with patches for ColabFold. This package allows running AlphaFold2 predictions (as published in Nature) with ColabFold enhancements. Current version 2.3.13. Release cadence is irregular, tied to AlphaFold updates.","status":"active","version":"2.3.13","language":"python","source_language":"en","source_url":"https://github.com/sokrypton/alphafold","tags":["alphafold","colabfold","protein-structure","deep-learning","bioinformatics"],"install":[{"cmd":"pip install alphafold-colabfold","lang":"bash","label":"PyPI install"}],"dependencies":[],"imports":[{"note":"AlphaFold is not a class in this package; model is accessed via alphafold.model.model","wrong":"from alphafold import AlphaFold","symbol":"AlphaFold2","correct":"from alphafold.model import model as alphafold_model"},{"note":"run_alphafold is specifically in the colabfold module","wrong":"from alphafold import run_alphafold","symbol":"run_alphafold","correct":"from alphafold.colabfold import run_alphafold"}],"quickstart":{"code":"from alphafold.colabfold import run_alphafold\nimport os\n# Set environment variables for required paths\nos.environ['ALPHAFOLD_DB_DIR'] = '/path/to/databases'  # Adjust to your DB path\nos.environ['ALPHAFOLD_MODEL_DIR'] = '/path/to/models'  # Adjust to your model params\n# Basic usage\nrun_alphafold(\n    fasta_path='sequence.fasta',\n    output_dir='./output',\n    num_models=1,\n    model_names='model_1',\n    use_amber=True,\n    use_gpu_relax=True\n)","lang":"python","description":"Minimal example to run AlphaFold2 prediction using ColabFold patched pipeline. You must have AlphaFold databases and model parameters downloaded."},"warnings":[{"fix":"pip uninstall alphafold && pip install alphafold-colabfold","message":"The package name 'alphafold-colabfold' may be confused with the older 'alphafold' package. Ensure you install 'alphafold-colabfold' specifically to get ColabFold patches.","severity":"breaking","affected_versions":"all"},{"fix":"Follow the AlphaFold setup guide at https://github.com/google-deepmind/alphafold to download databases and parameters, then set ALPHAFOLD_DB_DIR and ALPHAFOLD_MODEL_DIR environment variables.","message":"The run_alphafold function requires pre-downloaded AlphaFold databases (e.g., BFD, MGnify, PDB70, PDB, Uniref30, Uniclust30, etc.) and model parameters. The package does not download them automatically.","severity":"gotcha","affected_versions":"all"},{"fix":"Keep using use_amber=True unless future release notes indicate removal.","message":"The use_amber flag may be deprecated in future versions. The ColabFold patches recommend using 'use_amber=True' for better accuracy, but check notes on potential deprecation.","severity":"deprecated","affected_versions":"2.x"}],"env_vars":null,"last_verified":"2026-05-01T00:00:00.000Z","next_check":"2026-07-30T00:00:00.000Z","problems":[{"fix":"pip install alphafold-colabfold","cause":"Misspelled or wrong package installed; package is 'alphafold-colabfold' not 'alphafold'.","error":"ModuleNotFoundError: No module named 'alphafold'"},{"fix":"Use one of the following model names: 'model_1', 'model_2', 'model_3', 'model_4', 'model_5' or 'model_1_ptm', 'model_2_ptm', etc. Check the parameter directory.","cause":"Model name must match one of the available model filenames (e.g., 'model_1' is for CASP14, but actual parameter file might be named differently).","error":"ValueError: No such model: 'model_1'"}],"ecosystem":"pypi","meta_description":null,"install_score":null,"install_tag":null,"quickstart_score":null,"quickstart_tag":null}