Skip to main content
Glama

Search Target Literature

SearchTargetLiterature
Read-onlyIdempotent

Search PubMed for structural biology and drug design papers on binding site characterization, allosteric mechanisms, resistance mutations, and prior design campaigns to guide binder design.

Instructions

Search PubMed for recent structural biology and drug design papers.

Focuses specifically on binding site characterization, allosteric mechanisms, resistance mutations, and prior design campaigns — the literature most relevant to planning a new binder design effort.

Use the optional context parameter to narrow results, e.g.:

  • context='allosteric' for allosteric site literature

  • context='resistance' for resistance mutation papers

  • context='antibody' for biologic-focused papers

  • context='oncology' for disease-specific context

Call this LAST — after CharacterizeTarget, GetRelatedStructures, GetBindingSites, GetLigandHistory, and CheckConservation — to see if the literature reveals insights not captured in database records (e.g., cryptic sites found by MD simulation, unpublished allosteric mechanisms).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
contextNo
gene_nameYes
max_resultsNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

A4.3/5.0
Behavior4/5

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

Annotations already cover the safety profile (readOnly, idempotent, non-destructive, openWorld). The description adds the behavioral trait that matters most here: this is an external literature source used as a final cross-check after internal databases, which cannot be inferred from annotations. It omits any note on result freshness or rate limits, keeping it short of a 5.

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?

Front-loads the purpose in the first sentence, then uses compact bullets for context values and a clearly signposted ordering instruction. Slightly verbose in repeating 'most relevant to planning a new binder design effort', but every block is scannable and useful.

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?

An output schema exists, so return-format explanation is unnecessary; the description closes the remaining gap by defining scope, context options, and call ordering. Only the undocumented `max_results` behavior leaves a minor hole.

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 0%, so the description carries the burden and does partly compensate by enumerating four meaningful `context` values (allosteric, resistance, antibody, oncology). However, `gene_name` and `max_results` receive no explanation at all, so the compensation is incomplete.

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?

States a specific verb (Search) and resource (PubMed literature) plus the topical scope: binding site characterization, allosteric mechanisms, resistance mutations, prior design campaigns. No sibling tool covers literature, so the differentiation is implicit but unmistakable against the database-oriented siblings.

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

Usage Guidelines5/5

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

Explicitly instructs 'Call this LAST — after CharacterizeTarget, GetRelatedStructures, GetBindingSites, GetLigandHistory, and CheckConservation' and explains why (to catch insights not captured in database records, e.g. cryptic sites from MD). That is both when-to-use and sequencing guidance against named alternatives.

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