Rcsb Pdb

Search

search

Read-onlyIdempotent

"Find protein structure of [target]" / "search PDB for [protein]" / "is there a crystal structure of [X]" / "[disease target] structures" / "CRISPR / kinase / GPCR structures" — text search the RCSB PDB (the global archive of experimentally-determined 3D protein/RNA/DNA structures). Returns matching PDB IDs you can pass to structure or summary. Use for structural biology, drug design, protein characterization.

Input Schema

Name	Required	Description
`limit`	No	1-1000 (default 25).
`query`	Yes	Free-text, e.g. "CRISPR Cas9".
`return_type`	No	entry (default) \| polymer_entity \| non_polymer_entity \| assembly

Output Schema

Name	Required	Description	Default
`query_id`	No
`result_set`	No
`result_type`	No
`total_count`	No

Schema Changelog

Changes observed during successful MCP inspections.

Changed6 schema fields changedOct 20, 2026

removedOutput schema / properties / hits

Removed value: -{
-  "description": "Total number of hits matching the query",
-  "type": "number"
-}

addedOutput schema / properties / query_id
```
Added value: +{
+  "type": "string"
+}
```

addedOutput schema / properties / result_set

Added value: +{
+  "items": {
+    "properties": {
+      "identifier": {
+        "type": "string"
+      },
+      "score": {
+        "type": "number"
+      }
+    },
+    "type": "object"
+  },
+  "type": "array"
+}

addedOutput schema / properties / result_type
```
Added value: +{
+  "type": "string"
+}
```

removedOutput schema / properties / results

Removed value: -{
-  "description": "Array of matching entries/entities",
-  "items": {
-    "description": "Result object from RCSB search API",
-    "type": "object"
-  },
-  "type": "array"
-}

addedOutput schema / properties / total_count
```
Added value: +{
+  "type": "number"
+}
```

First observedJun 26, 2026

TDQS

A4.2/5.0

Behavior4/5

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

Annotations already declare readOnly, idempotent, non-destructive, open-world behavior, so the safety profile is covered. The description adds genuinely useful context beyond that: it operates over a specific external archive and returns PDB IDs intended for handoff to `structure`/`summary`, clarifying the search→retrieve workflow.

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

Conciseness4/5

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

Front-loading with example queries is an effective way to convey intent, followed by a compact resource definition and downstream routing. It's efficient, though the cluster of example strings is slightly denser than a prose opener and repeats the 'structures' framing.

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

Completeness5/5

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

With 100% schema coverage and an output schema present, the description needn't restate parameters or return shapes. It covers what the tool does, the data source, the output type (PDB IDs), and how to continue the workflow, which is everything an agent needs to select and invoke it correctly.

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

Parameters3/5

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

Schema description coverage is 100%, so the schema already documents query, limit, and return_type along with examples. The description adds no parameter-level detail (no query syntax, return_type semantics), leaving the schema to do all the work — the baseline 3 is appropriate.

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?

States a specific verb and resource ('text search the RCSB PDB'), defines the archive concretely (global archive of experimentally-determined 3D protein/RNA/DNA structures), and distinguishes itself from siblings by naming the follow-up tools `structure` and `summary`. An agent can immediately tell this is the discovery/front-door tool versus the retrieval tools.

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?

Provides concrete example phrasings ('find protein structure of [target]', 'CRISPR / kinase / GPCR structures') and states use cases (structural biology, drug design, protein characterization), plus routes downstream to `structure`/`summary`. It lacks an explicit when-not statement, but the context is clear enough to be actionable.

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

All Rcsb Pdb tools Inspect

Try in Browser

One endpoint for every MCP toolRayrun runs every MCP server behind one URL and holds the credentials. Each call is decided per client, tool, and argument, then recorded.ray.runAd

Glama MCP Gateway

Add one secure layer between your agents and this server.