protein-detective
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Python package to detect proteins in EM density maps.
Updated 3 months ago
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protein-quest
Python package to search/retrieve/filter proteins and protein structures
3
contributors
Cite this software
Description
Python package to search/retrieve/filter proteins and protein structures.
It uses
- Uniprot Sparql endpoint to search for proteins and their measured or predicted 3D structures.
- Uniprot taxonomy to search for taxonomy.
- QuickGO to search for Gene Ontology terms.
- gemmi to work with macromolecular models.
- dask-distributed to compute in parallel.
An example command:
protein-quest search uniprot \
--taxon-id 9606 \
--reviewed \
--subcellular-location-uniprot nucleus \
--subcellular-location-go GO:0005634 \
--molecular-function-go GO:0003677 \
--limit 100 \
uniprot_accs.txt
Participating organisations
Contributors
SV
Netherlands eScience Center
AE
Anna Engel
@UtrechtUniversity
AB
Alexandre Bonvin
@UtrechtUniversity
Related projects
Protein Detective
A software for AI-driven identification of unknown proteins in cryo-EM density maps
Updated 7 months ago
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