protein-tools-mcp

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query_metal_sites

Search the PDB-wide metal-site index by metal, geometry, and coordination number to find zinc fingers, catalytic zinc, or similar protein metal-binding sites.

Instructions

Search the PDB-wide metal-site index (premium: requires the hosted relay — set PROTEIN_TOOLS_RELAY_URL + PROTEIN_TOOLS_API_KEY).

Filter by metal, geometry class, coordination-number range. Defaults exclude CN-0 isolated-ion artifacts and CN-1; set min_cn=1 to see unusual CN-1 chemistry, include_artifacts=True to also return CN-0 rows. Examples: tetrahedral Cys4 zinc fingers (metal='ZN', geometry='tetrahedral'), catalytic zinc (metal='ZN', min_cn=4, max_cn=6).

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": {
      "metal": "<metal>"
    },
    "name": "query_metal_sites"
  }
}

Input Schema

Name	Required	Description	Default
`limit`	No
`metal`	Yes
`max_cn`	No
`min_cn`	No
`db_path`	No
`geometry`	No
`include_artifacts`	No

Output Schema

Name	Required	Description	Default
`result`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Oct 20, 2026

TDQS

A4.4/5.0

Behavior4/5

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 well: it discloses the premium/auth requirement (relay URL + API key) and the important default behavior that CN-0 and CN-1 rows are excluded unless overridden. It omits rate limits or failure behavior when the relay is unavailable, keeping it shy of a 5.

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?

Front-loaded with purpose, then the auth prerequisite, then filter semantics, then worked examples. Every sentence earns its place and nothing is redundant with the name or title.

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?

An output schema exists, so return values need not be described; against the moderate schema complexity the description covers auth, defaults, overrides, and examples. The only residual gaps are the meaning of db_path and the limit parameter, which are minor for an otherwise complete definition.

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 coverage is 0%, so the description must compensate and largely does: it explains metal, geometry, min_cn, max_cn, and include_artifacts with defaults and semantics. It leaves limit and db_path (both present in the schema) unexplained, so it does not fully close the 7-parameter gap.

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?

Specific verb (Search) plus a precisely scoped resource (the PDB-wide metal-site index), and the filter dimensions (metal, geometry, coordination number) tell an agent exactly what kind of query this is. It is distinguishable from siblings like metal_geometry and check_metal_params by being an index-level search rather than a single-structure analysis.

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?

It clearly states when and how to use it: filter by metal/geometry/CN range, and it explains the default filtering behavior and how to override it (min_cn=1, include_artifacts=True). Two concrete examples (Cys4 zinc fingers, catalytic zinc) reinforce the intended usage, though no sibling alternatives are explicitly named.

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