Skip to main content
Glama
Biochemistry Archive MCP Server

Biochemistry Archive MCP Server

by AudreyZW

find_ligands

Retrieve known binders for a target with measured potency, ranked most potent first, using a ChEMBL target ID or UniProt accession.

Instructions

Known binders of a target with measured potency, most potent first. Takes a ChEMBL target id or a UniProt accession.

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": {
      "target": "<target>"
    },
    "name": "find_ligands"
  }
}

Input Schema

NameRequiredDescriptionDefault
limitNo
targetYesChEMBL target id ('CHEMBL203') or UniProt accession
assay_typeNoRestrict to one assay type, e.g. 'IC50', 'Ki', 'Kd', 'EC50'. Casing is normalised for you.
min_potencyNoMinimum pChEMBL value; 8 is ~10 nM

Output Schema

NameRequiredDescriptionDefault

No arguments

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

B3.4/5.0
Behavior3/5

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

With no annotations, the description carries the full burden, but it does disclose useful behavior: results are ordered most-potent-first and potency is a measured value. It omits data provenance (ChEMBL assays), what happens when no binders are found, and result-count behavior; the presence of an output schema offsets the missing return-format detail.

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?

Two short sentences with no filler, and the ordering guarantee is front-loaded where it matters. Slightly thin rather than padded, which is the right failure mode.

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

Completeness3/5

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

Adequate for a read-style lookup: the output schema covers return values and the input schema covers most parameters. Missing is behavioral context an agent would want, such as whether an empty result is normal, whether the target must be resolved via find_target first, and the data source.

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 75%, so the schema already documents target format, assay_type examples, and min_potency scaling. The description repeats the target id/accession formats rather than adding meaning, and says nothing about limit or how assay_type interacts with the potency ordering.

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 resource and what it returns: 'Known binders of a target with measured potency, most potent first.' That is concrete enough to distinguish it from siblings like find_target or get_structures, though it never names those siblings explicitly.

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

Usage Guidelines3/5

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

Usage is only implied: an agent can infer 'use this when you have a target id and want known binders with potency.' There is no explicit when-not guidance, no mention of alternatives such as get_structures or compare_compounds, and no prerequisites such as requiring a resolved target first.

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