ligand"Ligand / cofactor / drug bound to [pdb_id]" / "small molecule in [PDB entry]" — fetch a non-polymer ligand record (small molecule, cofactor, ion, or bound drug) for a PDB entry. Use to inspect what's bound in a co-crystal structure — common in drug discovery / SBDD.
| Name | Required | Description | Default |
|---|---|---|---|
| pdb_id | Yes | ||
| ligand_id | Yes |
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||
Changes observed during successful MCP inspections. Dates show when Glama detected each change.
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint=true and destructiveHint=false, so the description doesn't need to restate safety. It adds context about the entity type (non-polymer, small molecule, cofactor, ion, drug) but does not disclose additional behavioral traits like error handling, rate limits, or return behavior beyond what annotations imply.
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?
The description is somewhat repetitive, opening with two alternative quoted phrases ('Ligand / cofactor / drug bound to [pdb_id]' / 'small molecule in [PDB entry]') that overlap with the main explanation. It is not excessively long but could be more streamlined. This warrants a middle score.
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?
Given that the tool has only two parameters, read-only annotations, an output schema, and a clear domain context (co-crystal structures, SBDD), the description provides sufficient information for a simple fetch operation. It explains the parameter roles and usage context, making it reasonably complete without needing to detail return values.
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?
The input schema has 0% description coverage, so the description compensates by explaining pdb_id as a PDB entry and ligand_id as the bound small molecule/ligand. It clarifies the roles of both parameters in context, though it doesn't specify exact formats or code conventions (e.g., 4-character PDB code or HET code), preventing a 5.
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 fetches a non-polymer ligand record (small molecule, cofactor, ion, or bound drug) for a PDB entry, using a specific verb ('fetch') and resource ('non-polymer ligand record'). It distinguishes from siblings by explicitly highlighting 'non-polymer' and listing entity types, contrasting with potential polymer-related tools.
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?
The description provides a clear use case: 'Use to inspect what's bound in a co-crystal structure — common in drug discovery / SBDD.' This gives context for when to use the tool, but it does not explicitly mention when not to use it or name alternative tools, so it falls short of a 5.
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.
ask_pipeworx, ask_pipeworx_beta, and ask_pipeworx_grounded are nearly identical in purpose, and structure/summary both fetch PDB entries. The server name 'Rcsb Pdb' doesn't match most tools, which are Pipeworx data tools, compounding ambiguity.
Mostly snake_case verb_noun, but verbs are inconsistent (ask, discover, generate, list, recall) and some names are noun phrases (entity_profile, polymarket_edges). No clear pattern unifies the set.
37 tools is excessive for a server ostensibly about RCSB PDB; only 6 tools relate to PDB while 31 serve unrelated Pipeworx functionality. The count feels like a bundled grab-bag rather than a focused toolset.
The PDB-specific tools cover the core operations (search, fetch, assembly, ligand, polymer entity), so the structural biology surface is mostly complete. However, the server's overall purpose is muddled, and the Pipeworx tools are a separate domain that happens to be bundled in, making it unclear what 'completeness' even means for this server.