PocketScout MCP

Characterize Target

CharacterizeTarget

Read-onlyIdempotent

Establish biological context for a drug target protein by retrieving function, family, location, disease links, and AlphaFold confidence; start here to guide downstream analysis.

Instructions

Establish biological context for a drug target protein.

Retrieves protein function, family classification, subcellular location, disease associations, and AlphaFold structure confidence. This should be your FIRST call — all downstream analysis depends on this context.

IMPORTANT: AlphaFold confidence flags regions where predicted structure is unreliable. Low-confidence regions (<70 pLDDT) may have incorrect pocket predictions — always cross-reference with experimental structures.

Provide EITHER a PDB ID (e.g. '1M17') OR a UniProt accession (e.g. 'P00533'). If a PDB ID is given, the UniProt mapping is resolved automatically.

Tool call template

This tool declares no required parameters. Add optional parameters from the input schema as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {},
    "name": "CharacterizeTarget"
  }
}

Input Schema

Name	Required	Description	Default
`pdb_id`	No
`uniprot_id`	No

Output Schema

Name	Required	Description	Default
No arguments

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Sep 13, 2026

TDQS

A4.6/5.0

Behavior4/5

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

Annotations already declare readOnly/idempotent/non-destructive, so safety is covered. The description adds meaningful domain-specific behavioral context beyond annotations: the AlphaFold confidence caveat (<70 pLDDT regions may yield incorrect pocket predictions) and the automatic PDB→UniProt resolution. This is valuable but doesn't cover rate limits or output caveats in depth.

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-loaded with the core purpose, then retrieval scope, the first-call directive, the AlphaFold caveat, and the input rule. It is somewhat longer than strictly necessary (the AlphaFold IMPORTANT paragraph is a sizeable aside) but every block carries useful information and nothing is filler.

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?

For a read-only characterization tool with an output schema present, the description covers purpose, retrieval contents, call ordering, and the input contract. The AlphaFold caveat pre-empts downstream misuse, and return values needn't be explained since an output schema exists.

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?

Schema description coverage is 0%, so the description must compensate — and it does: it gives concrete example values ('1M17', 'P00533') and states the resolution behavior when a PDB ID is provided. Both parameters are addressed, though it doesn't clarify precedence if both are supplied or that both are optional.

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 opens with a specific verb+resource: 'Establish biological context for a drug target protein', then enumerates exactly what is retrieved (function, family, subcellular location, disease associations, AlphaFold confidence). This makes the tool's scope unambiguous and clearly distinguishable from siblings like GetBindingSites or SearchTargetLiterature.

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

Usage Guidelines5/5

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

Explicitly instructs 'This should be your FIRST call — all downstream analysis depends on this context', giving a clear ordering prerequisite relative to the sibling analysis tools. The either/or input rule ('Provide EITHER a PDB ID OR a UniProt accession') further guides correct invocation.

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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