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Biochemistry Archive MCP Server

Biochemistry Archive MCP Server

by AudreyZW

find_target

Resolve a protein or gene name to its UniProt accession, experimental structure count, and matching ChEMBL target. Use the returned accession as the key for related biochemistry tools.

Instructions

Resolve a protein or gene name to a UniProt accession, with the number of experimental structures and the matching ChEMBL target. Start here: the accession returned is the key the other tools take.

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": {
      "query": "<query>"
    },
    "name": "find_target"
  }
}

Input Schema

NameRequiredDescriptionDefault
limitNo
queryYesProtein or gene name, e.g. 'EGFR'
organism_idNoNCBI taxon id; 9606 is human. None searches all species.

Output Schema

NameRequiredDescriptionDefault

No arguments

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

A4/5.0
Behavior3/5

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

With no annotations, the description must carry behavioral weight. It does disclose the workflow role and the content of the result (accession, structure count, ChEMBL target), but says nothing about ambiguous-name behavior, what happens when no target is found, or that the lookup relies on external UniProt/ChEMBL data. Useful context, but incomplete for a zero-annotation tool.

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?

Two sentences, front-loaded with the core purpose and followed immediately by the dependency-based usage rule. No filler wording.

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 the description need not restate return fields in detail, and the schema covers most parameters. Remaining gaps are ambiguity handling and the limit parameter. Overall sufficient for an agent to call this first in the workflow.

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 coverage is 67%: query has an example and organism_id explains the taxon id and the None behavior. The description adds only the notion of 'protein or gene name' and does not clarify the undocumented limit parameter or say how multiple matches are ranked. Baseline 3 is appropriate since the schema does most of the work.

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 transformation: resolve a protein or gene name to a UniProt accession, and names the two additional outputs (experimental structure count, matching ChEMBL target). This is clearly distinguishable from siblings like get_structures and find_ligands, which consume rather than produce the accession.

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?

Explicitly says 'Start here' and explains why: the returned accession is the key the other tools take. That gives a clear entry-point rule relative to siblings. It stops short of when-not guidance (e.g. what to do if the query is ambiguous or the target is already known), so not a 5.

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