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Protein Binding Pocket

protein_binding_pocket
Read-onlyIdempotent

Summarizes candidate binding pockets from UniProt functional annotations and AlphaFold confidence scores to identify potential protein binding sites.

Instructions

Summarize candidate binding sites from UniProt functional-site annotations plus AlphaFold confidence context.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
accessionNoUniProt accession.
queryNoProtein or gene query used to resolve a reviewed accession.
max_sitesNoMaximum candidate sites to return. Default 10.
Behavior4/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false, idempotentHint=true, and openWorldHint=true. The description adds valuable context about data sources (UniProt and AlphaFold) and the summarization behavior, enhancing understanding beyond annotations.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is a single concise sentence that efficiently conveys the tool's purpose without unnecessary words or repetition.

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 tool has 3 parameters (all optional), no output schema, and annotations indicating read-only behavior, the description adequately covers what the tool does and its data sources. However, it lacks details on output format or what 'summarize' entails.

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% and all parameters are well-described in the schema. The description adds general context about the tool's output but does not provide specific additional meaning for the parameters beyond what the schema includes.

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?

The description clearly states the verb 'summarize', the resource 'candidate binding sites', and the data sources 'UniProt functional-site annotations plus AlphaFold confidence context'. It effectively distinguishes this tool from siblings like get_alphafold_structure or find_protein.

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?

The description implies usage for summarizing binding sites but does not explicitly state when to use this tool vs. alternatives, nor does it provide when-not-to-use guidance or mention prerequisites.

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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