Retrieve AlphaFold Protein Structure

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint=true, idempotentHint=true, openWorldHint=true, so safety is covered; the description goes further by enumerating returned fields (entry ID, pLDDT, download URLs), flagging the legacy-only PAE image URL, warning that coordinates are large, and documenting the structure_available:false coverage-gap behavior. That is meaningful context beyond the structured fields.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Is the description appropriately sized, front-loaded, and free of redundancy?

Front-loaded with the core purpose and the key routing rule, then returns and edge cases. Every section earns its place, though the field enumeration and the four-sibling list make it longer than strictly necessary for a single-parameter read tool.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

With annotations, an output schema, and nested params already present, the remaining burden is edge-case behavior and routing — both covered (structure_available:false, legacy PAE image caveat, non-overlapping sibling scopes). Nothing an agent needs to call this correctly is missing.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is reported as 0% at the top level, but the nested parameter descriptions are actually informative; the description reinforces include_coordinates by explaining it embeds the full PDB coordinate text and that it is large. It adds size/behavior guidance beyond a bare boolean, though it does not add anything about uniprot_id format.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Does the description clearly state what the tool does and how it differs from similar tools?

Starts with a specific verb+resource ('Retrieve a protein's AlphaFold model') and explicitly calls itself 'the single entry point for getting the predicted structure itself,' which cleanly separates it from siblings that interpret structures. An agent can identify this as the retrieval tool without opening the schema.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Does the description explain when to use this tool, when not to, or what alternatives exist?

States the when-to-use rule directly ('use the sibling structure tools for interpretation rather than retrieval') and names four alternatives with their distinct scopes: analyze_structural_confidence, score_binding_pocket_geometry, compute_topology_fingerprint, detect_intrinsically_disordered. This is explicit routing, not inference.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.