Protein¶

Use protein commands to query UniProt accessions and expand into domains, interactions, complexes, and structure IDs.

Search proteins¶

biomcp search protein -q kinase --limit 5

Search is human-only and reviewed-only by default. Species and review scope are independent: add --all-species without changing review quality, or add --include-unreviewed without changing the human scope. The two flags may be combined. --reviewed remains an explicit spelling of the default and conflicts with --include-unreviewed.

Get protein records¶

biomcp get protein P15056

Request protein sections¶

Domains:

biomcp get protein P15056 domains

Interactions:

biomcp get protein P15056 interactions

Complexes:

biomcp get protein P15056 complexes

Complexes render as a narrow summary table first, then one bounded member-preview bullet per complex so long names and large memberships stay readable in a terminal.

## Complexes

| ID | Name | Members | Curation |
|---|---|---:|---|
| CPX-13454 | BRAF:DELE1 stress-response complex | 2 | predicted |
- `CPX-13454` members (2): DELE1, BRAF

Structures:

biomcp get protein P15056 structures

Helper commands¶

biomcp protein structures P15056

JSON mode¶

biomcp --json get protein P15056 all

Optional-section outcomes¶

JSON and MCP protein records include outcomes for domains, interactions, complexes, and structures. Unrequested keys are not_requested; a requested empty vector is a confirmed zero only when its outcome is empty. Provider failure is unavailable and is also reported in Markdown.

Practical tips¶

Use a UniProt accession when you need the most stable exact lookup.
Follow JSON pagination.next_offset while has_more is true; it is omitted at the end.
Request only the section you need first, especially for interactions and complexes.
Use protein structures when the next step is a structure handoff rather than a full protein card.

Gene
Pathway