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KrithikVishal

Biomedical APIs MCP Server

Search ChEMBL Compounds

search_chembl_compounds

Search ChEMBL database to find small molecules using their name or SMILES string. Retrieve compound information to support drug discovery research.

Instructions

Search ChEMBL for small molecules by name or SMILES

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNoNumber of results
queryYesMolecule name or SMILES string

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
compoundsYes
Behavior2/5

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

No annotations provided, so description carries full burden. It only states the basic function, missing important behavioral traits like authentication needs, rate limits, or behavior when no results found.

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?

Single sentence, concise and front-loaded. No unnecessary words; every part serves the purpose.

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?

With output schema present, return values don't need explanation. However, lacks information on handling multiple matches, pagination, or result interpretation. Adequate for a simple search but could be improved.

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 100% with descriptions for both parameters. The description adds marginal value by mentioning 'by name or SMILES' which aligns with the query parameter, but does not provide additional meaning beyond schema.

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?

Description clearly states verb 'Search', resource 'ChEMBL for small molecules', and query types 'by name or SMILES'. It distinguishes from siblings like get_chembl_activities which retrieves activities for a specific compound.

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?

Implied usage for searching molecules by name or SMILES, but no explicit guidance on when to use this tool vs alternatives like get_pubchem_compound or query_bindingdb. Sibling list shows many data sources without differentiation.

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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