get_moleculesPDBe (EBI): list the molecules/entities in a PDB structure — proteins, nucleic acids, and ligands, each with entity_id, molecule_type, name, and chain length. Keyless. Pass a 4-char PDB id like "1cbs".
| Name | Required | Description | Default |
|---|---|---|---|
| pdb_id | Yes | A 4-char PDB id, e.g. "1cbs". |
Changes observed during successful MCP inspections. Dates show when Glama detected each change.
Input schema / examplesAdded value: +[
+ {
+ "pdb_id": "1cbs"
+ },
+ {
+ "pdb_id": "4hhb"
+ }
+]Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Beyond annotations (readOnly, openWorld, etc.), description adds key details: keyless access, source (PDBe/EBI), and return fields, enhancing transparency.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Two sentences with no waste; critical information (purpose, input, output) is front-loaded and efficiently presented.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Despite no output schema, description sufficiently describes return fields. With one simple parameter, the tool is fully specified for an agent.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema covers 100% of parameters with description, and description only reiterates the example, adding no new semantics beyond what's in schema.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the tool lists molecules/entities in a PDB structure with specific fields, distinguishing its purpose from siblings that are unrelated.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
Provides explicit context on when to use (need molecule info from PDB) and input format (4-char PDB id), but lacks when-not or alternatives, though siblings are unrelated.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Add one secure layer between your agents and this server.
Many tools overlap in purpose: ask_pipeworx, ask_pipeworx_grounded, ask_pipeworx_beta, and deep_research all perform similar data lookups with slight variations. Prediction market tools (bet_research, polymarket_arbitrage, polymarket_edges) also overlap. Only the three PDBe-specific tools are clearly distinct, but overall the set is confusing.
Tool names follow no consistent pattern: some are verb_noun (ask_pipeworx, get_molecules), others are noun_verb (ai_visibility_check), or have mixed conventions (generate_llms_txt, uniprot_mappings). The variety of verbs (ask, bet, compare, discover, generate, get, list, recall, remember) makes it hard to predict tool names.
With 34 tools, the server is overstuffed for a single domain. It mixes PDBe-specific tools (3) with a large set of general-purpose data tools, prediction market tools, subscriptions, and memory tools. This bloat suggests the server should be split into focused services.
For the stated PDBe domain, only three tools exist (get_molecules, get_summary, uniprot_mappings), missing essential operations like search, download, or advanced queries. The server's overall purpose is unclear, and it feels like a random collection of tools rather than a coherent API.