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pdb

Search the Protein Data Bank by query or PDB ID to retrieve macromolecular structure metadata and download structure files in mmCIF or PDB format.

Instructions

Access the Protein Data Bank (RCSB PDB) for macromolecular structure data.

SEARCH: Provide "query" to find structures (e.g., "kinase inhibitor", "hemoglobin"). GET: Provide "pdb_id" to retrieve entry metadata with optional detail sections. DOWNLOAD: Provide "pdb_id" + download=true to save the structure file and get the file path.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
queryNoFree-text search query to find PDB entries. Omit pdb_id when searching.
pdb_idNoPDB identifier (e.g., "1CRN", "4HHB"). Required for get/download.
sectionsNoMetadata sections: polymer_entities (chains and sequences), ligands (small molecules and ions), assembly (biological assembly), experiment (method, resolution), citation (publication). Use "all" for everything. Default: core summary only.
downloadNoSave the structure file to disk and return the file path. Only used with pdb_id.
formatNoFile format: "cif" (mmCIF, recommended, always available) or "pdb" (legacy format, may not exist for some entries). Only used with download=true.cif
limitNoMax search results
offsetNoSearch result offset
Behavior4/5

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

Annotations convey openWorldHint=true and readOnlyHint=false, and the description adds context about the download side effect (saving a file to disk). This clarifies behavioral traits beyond the structured annotations. No contradictions.

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

Conciseness5/5

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

The description is extremely concise, using three short sentences to convey three modes of operation. It is front-loaded with the tool's purpose and uses line breaks for readability. No superfluous information.

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

Completeness3/5

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

Given the tool has 7 parameters and no output schema, the description partially compensates by explaining parameter usage for each mode. However, it does not specify the return format for search and get results (e.g., what data structure is returned) or error handling. This leaves some ambiguity for an AI agent.

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

Parameters4/5

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

Input schema has 100% description coverage, so baseline is 3. The description adds significant value by grouping parameters into modes (SEARCH, GET, DOWNLOAD) and explaining inter-parameter dependencies (e.g., download only used with pdb_id). This enhances understanding beyond individual parameter descriptions.

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

Purpose5/5

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

The description clearly states it accesses the Protein Data Bank for macromolecular structure data and enumerates three distinct operations (SEARCH, GET, DOWNLOAD) with specific verbs and resources. It distinguishes itself from siblings which focus on other data types like articles, diseases, etc.

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

Usage Guidelines4/5

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

The description provides explicit mapping of parameters to operations: query for searching, pdb_id for get/download, and download=true for saving files. It explains when to omit parameters. However, it does not explicitly state when not to use this tool or alternative tools, though the sibling context makes it implicit.

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

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