protein-quest

protein-quest searches, retrieves, and filters proteins and protein structures.

Key Features:

• Protein search and retrieval: Searches and retrieves proteins and protein structures from databases.
• Protein filtering: Filters protein datasets based on specified criteria.
• Structure retrieval from PDBe: Retrieves protein structures from the Protein Data Bank in Europe (PDBe) with optional --beta-archive flag.
• Structure retrieval from AlphaFold: Retrieves AlphaFold-predicted structures with optional --write-stats output.
• Structure writing with chemical components: Includes chemical component information in written structures for enhanced Mol* tooltips.
• UniProt accession handling: Reads and writes UniProt accessions directly from the _pdbx_sifts_unp_segments mmCIF category.
• Statistics output: Generates statistics files via --write-stats for PDBe and AlphaFold retrieval operations.

Scientific Applications:

• Protein structure analysis: Enables systematic access to experimental and predicted protein structures for structural biology research.
• Structural bioinformatics pipelines: Supports automated retrieval and processing of protein structure data for downstream computational analyses.
• Structure visualization preparation: Prepares structure files with chemical component annotations for visualization in molecular viewers such as Mol*.

Methodology:

protein-quest implements Python-based commands to query protein databases, process mmCIF format files containing _pdbx_sifts_unp_segments categories, and write structure files with chemical component annotations.