By tool¶
One-shot examples, roughly one per tool, showing what each tool is for on its own. The agent picks the tools itself from their descriptions; seeing the mapping helps you understand what the server can do.
Identify an unknown domain from a keyword¶
Prompt: “I keep seeing ‘kringle domain’ in papers. What is it, and what InterPro entry describes it?”
Tools: searchInterPro → getEntry
Free-text search has no accession to start from, so the agent searches for kringle domain,
finds candidate entries, then pulls full metadata (definition, GO terms, member signatures,
literature) for the best hit, InterPro IPR000001.
Look up a signature and place it on the tree of life¶
Prompt: “What is Pfam PF00069, and is it mostly a eukaryotic or a bacterial domain?”
Tools: getEntry → getTaxonomicDistribution
getEntry resolves PF00069 to the protein-kinase domain (integrated into IPR000719).
getTaxonomicDistribution with depth: 1 returns the superkingdom breakdown: the domain is
overwhelmingly eukaryotic, without downloading the large full species-level tree.
Annotate a UniProt protein¶
Prompt: “What domains are in UniProt P99999, and where are they?”
Tools: getProteinEntries
One call fetches the sequence, computes its MD5, and returns every matching member-database signature and integrated InterPro entry with residue locations.
Go from a function (GO term) to the domains that carry it¶
Prompt: “Which InterPro entries are annotated with the protein-kinase activity term GO:0004672?”
Tools: searchByGoTerm
Returns the InterPro entries associated with that molecular-function term, paginated.
Find example proteins for a domain, filtered to a species¶
Prompt: “List some reviewed human proteins that contain the kringle domain IPR000001.”
Tools: getEntryProteins
With reviewedOnly: true and taxId: "9606", the agent gets Swiss-Prot human proteins
carrying the domain (plasminogen, prothrombin, HGF, etc.), each with the matched residue ranges
and an AlphaFold-model flag.
Find structural representatives of a domain¶
Prompt: “What PDB structures contain the protein-kinase domain PF00069?”
Tools: getEntryStructures
Returns the PDB entries that include the domain: PDB id, title, experiment type, resolution, and where in each structure the domain maps.
Understand the context a domain appears in¶
Prompt: “What domain architectures does the Tubby domain IPR000007 occur in?”
Tools: getDomainArchitectures
Returns the recurring ordered domain combinations the entry is part of across UniProt, each with a representative protein and how many proteins share that architecture.
Analyse a brand-new sequence¶
Prompt: “Run InterProScan on this sequence and tell me what domains it has:
MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE”
Tools: analyzeSequence → getSequenceAnalysis
Because the sequence may not be in InterPro’s precomputed set, the agent runs a live
InterProScan 6 job on the EMBL-EBI Job Dispatcher. analyzeSequence submits and waits a bounded
time; if the job finishes it returns the full result, otherwise a jobId the agent retrieves
a moment later with getSequenceAnalysis. The verdict here: a cytochrome c domain (Pfam
PF00034, InterPro IPR009056 / IPR036909).
Screen a batch of sequences¶
Prompt: “Here are 20 protein sequences. Which already have precomputed InterPro matches?”
Tools: matchSequences
Looks up all of them in one call (up to 100), keyed by MD5, reporting for each whether it was found and its matches.