find_pdb_by_sequence

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

With no annotations, the description carries the full behavioral burden and does reasonably well: it discloses the FASTA parsing step, the type-to-program mapping (blastp/blastn), that PDB IDs are returned, that ambiguous sequences fail with a structured error, and that an API key is required (premium). Cost/rate-limit details and whether results are ranked are unstated.

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?

Four tight sentences, front-loaded with the core action and progressively adding mapping, error, and auth details. No filler; every sentence adds actionable information.

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?

An output schema exists, so return-value explanation is unnecessary, and behavioral/auth context is present. However, for a 4-parameter tool with 0% schema coverage, the absence of any parameter semantics leaves a real gap an agent would need to fill.

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 0% and the description explains none of the four parameters (source, is_file, max_results, sequence_index). The FASTA mention loosely touches source/is_file, but max_results and sequence_index are undocumented in both the schema and the description.

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?

States a specific verb+resource ('Find PDB structures matching a protein, DNA, or RNA sequence') and clarifies direction. It implicitly contrasts with the reverse-direction sibling sequence_from_pdb, but never names it or other related tools like rcsb_entry or detect_sequence_type.

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?

Usage is implied by the workflow described (parses FASTA, maps to BLAST search), but there is no explicit when-to-use guidance or routing against alternatives such as detect_sequence_type, read_fasta, or sequence_from_pdb. The premium/API-key note gives some context but no alternative selection logic.

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