Skip to main content
Glama
PDBeurope

PDBe MCP Servers

Official
by PDBeurope

get_molecules_api_pdb_entry_molecules__pdb_id__get

Read-only

Retrieve detailed information about each molecule in a PDB entry, including entity type, sequence data, chain assignments, and source organism.

Instructions

Returns summarised detailed information about each molecule (or entity in mmcif-speak) in a specified PDB entry, including entity type; molecule names mapped from UniProt; the synonym field (equivalent to _entity.pdbx_description) for polymeric entities; DrugBank-derived synonyms for ligands; sequence data; chain assignments; copy numbers; source organism and sample preparation details; and ligand or chemical component information.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pdb_idYes4-character PDB id code. title: Pdb Id description: 4-character PDB id code.
entity_idNoEntity id (molecule number in mmcif-speak).
Behavior3/5

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

Annotations already declare readOnlyHint=true, so the description's disclosure of returned data adds moderate value but does not cover additional behavioral traits or performance characteristics. The description is consistent with annotations.

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?

The description is a single, well-structured sentence that front-loads the core action ('Returns summarised detailed information about each molecule') and lists all included data fields efficiently. It is concise given the amount of information conveyed.

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?

Given the complexity of the returned data and the absence of an output schema, the description provides a comprehensive list of fields (entity type, UniProt names, sequence, chains, etc.), adequately setting expectations for the agent.

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 100%, so the baseline is 3. The description does not add extra meaning to the parameters beyond what the schema already provides (e.g., pdb_id format, entity_id as integer).

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?

The description clearly states it returns summarised detailed information about each molecule in a specified PDB entry, listing specific data fields. However, it does not explicitly differentiate from sibling tools like get_bound_molecules or get_ligand_summary, which limits clarity in a contextual toolset.

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

Usage Guidelines2/5

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

The description provides no guidance on when to use this tool versus alternatives. It does not mention prerequisites, intended use cases, or exclusions, leaving the agent to infer usage from the description alone.

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

Install Server

Other Tools

Latest Blog Posts

MCP directory API

We provide all the information about MCP servers via our MCP API.

curl -X GET 'https://glama.ai/api/mcp/v1/servers/PDBeurope/PDBe-MCP-Servers'

If you have feedback or need assistance with the MCP directory API, please join our Discord server