protein-detective

Python package to detect proteins in EM density maps.

Install

pip install protein-detective

Or to use the latest development version:

pip install git+https://github.com/haddocking/protein-detective.git

Usage

Search Uniprot for structures

protein-detective search \
    --taxon-id 9606 \
    --reviewed \
    --subcellular-location-uniprot nucleus \
    --subcellular-location-go GO:0005634 \
    --molecular-function-go GO:0003677 \
    --limit 100 \
    ./mysession

(GO:0005634 is "Nucleus" and GO:0003677 is "DNA binding")

In ./mysession directory, you will find session.db file, which is a DuckDB database with search results.

To retrieve a bunch of structures

protein-detective retrieve ./mysession

In ./mysession directory, you will find PDB files from PDBe and AlphaFold DB.

To filter AlphaFold structures on confidence

Filter AlphaFoldDB structures based on density confidence. Keeps entries with requested number of residues which have a confidence score above the threshold. Also writes pdb files with only those residues.

protein-detective density-filter \
    --confidence-threshold 50 \
    --min-residues 100 \
    --max-residues 1000 \
    ./mysession

To prune PDBe files

Make PDBe files smaller by only keeping first chain of found uniprot entry and renaming to chain A.

protein-detective prune-pdbs ./mysession

Contributing

For development information and contribution guidelines, please see CONTRIBUTING.md.