interpro-database

What it does

Retrieves and cross-links protein domain architecture, family classifications, taxonomy distributions, and structure data via the InterPro REST API. It supports searching entries, retrieving per-protein domain maps, listing proteins containing an InterPro entry, obtaining taxonomy summaries, and linking to PDB structures. It also includes utilities to fetch FASTA sequences for proteins in a given InterPro entry.

How it works

The skill provides concrete Python code blocks that:

• Define a base function interpro_get to perform GET requests to the InterPro API and parse JSON.
• Use entry/search endpoints to fetch InterPro entries by keyword or by accession, returning and printing metadata like accession, type, and name.
• Retrieve protein domain architectures for UniProt accessions from /entry/interpro/protein/uniprot/{acc}/, including per-entry nested protein locations and counts.
• Compare domain sets between two proteins by calling the domain-architecture function and computing set intersections and differences.
• List proteins containing a given InterPro entry via /protein/{db}/entry/interpro/{IPR}/, with an option to restrict to reviewed entries.
• Paginate all proteins for a family by repeatedly following the next link, collecting results.
• Get taxonomic distributions via /taxonomy/uniprot/entry/interpro/{IPR}/, and print top taxa with rank and names.
• Retrieve PDB structures linked to an InterPro entry via /structure/pdb/entry/interpro/{IPR}/, printing accession, resolution, and experiment type.
• Download FASTA sequences for proteins in a family by first collecting protein entries and then streaming FASTA from UniProt for the collected accessions.

When to use it

• When you need to identify all domains and families in a protein by UniProt accession (domain architecture)
• When you want to search for proteins containing a particular domain or family
• When you need taxonomic distribution for organisms encoding a given domain or family
• When you want to link a domain to experimental 3D structures in PDB
• When you want to discover InterPro entries by keyword or by accession
• When you need to retrieve UniProt sequences or to download domain-aligned sequences or build HMM profiles

What it can touch

• InterPro REST API endpoints at https://www.ebi.ac.uk/interpro/api
• Uniprot REST API endpoint https://rest.uniprot.org/uniprotkb/stream
• Local Python dependencies: requests, time, pandas (in examples), and standard JSON handling as shown in the code blocks

Caveats

• The Quick Start and code blocks depend on internet access and the InterPro API being available; there are notes about potential timeouts for large queries and the use of next cursors for pagination.
• The examples include a note that certain endpoints may time out for very large protein families; the code demonstrates iteration using the next URL and time.sleep between requests where applicable.
• The license is shown as CC-BY-4.0 in the skill metadata; no explicit license text is included in the snippet beyond that.