PocketScout MCP

Check Known Variants

CheckKnownVariants

Read-onlyIdempotent

Flag known disease or resistance variants and mutagenesis hits at binding-site residues using a UniProt accession and GetBindingSites positions. Highlights pockets that mutate under drug pressure.

Instructions

Flag known sequence variants and mutagenesis hits at binding-site residues.

Binding-site residues that are documented disease/resistance variants (e.g. EGFR T790M) mark pockets that mutate under drug pressure — a key risk signal when choosing where to design. Source: UniProt Natural variant + Mutagenesis features. Provide the human UniProt accession and positions from GetBindingSites.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "uniprot_id": "<uniprot_id>",
      "residue_positions": "<residue_positions>"
    },
    "name": "CheckKnownVariants"
  }
}

Input Schema

Name	Required	Description	Default
`uniprot_id`	Yes
`residue_positions`	Yes

Output Schema

Name	Required	Description	Default
No arguments

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Sep 13, 2026

TDQS

A3.9/5.0

Behavior4/5

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

Annotations already declare readOnly/idempotent/non-destructive/openWorld, so safety is covered. The description adds real behavioral context beyond that: the underlying data source (UniProt Natural variant + Mutagenesis features) and how to interpret a positive hit as a drug-resistance risk signal. Output format is deferred to the output schema.

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-loads the action, follows with the interpretation rationale, and ends with the concrete input instruction. Well-sized with no filler, though the middle explanatory sentence is somewhat long.

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

Completeness4/5

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

For a simple two-parameter read-only lookup with an output schema present, the description covers purpose, data provenance, and input sourcing sufficiently; an agent has what it needs to call it correctly. Minor gaps remain around position format.

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 0%, so the description carries the burden. It does add value by specifying the accession must be human and that residue_positions come from GetBindingSites, but it gives no format details such as numbering convention or expected position range, leaving meaningful ambiguity for a 2-parameter tool.

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

Purpose4/5

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

States a specific verb and resource: 'Flag known sequence variants and mutagenesis hits at binding-site residues.' It also names the upstream sibling (GetBindingSites) as the source of positions, which helps separate it from CharacterizeTarget/CheckConservation, though it never explicitly contrasts with those siblings.

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?

Gives clear context: call it with a human UniProt accession plus positions obtained from GetBindingSites, and explains why (documented variants mark pockets that mutate under drug pressure, a risk signal for design choices). No explicit when-not-to-use or exclusion of alternatives, so it stops short of a 5.

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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