CovaSyn Chemistry Tools

covabio_cleavage_sites

Map protease cleavage sites and score proteolytic stability. Covers trypsin (after K/R, not before P), chymotrypsin (after F/W/Y, not before P), pepsin (after F/L) and elastase (after A/G/S/V). Returns per-protease position lists, a total site count, a 0-100 stability score and a classification (highly_stable / moderate / proteolytically_labile).

Two uses: predicting in-vivo half-life and serum stability for a peptide therapeutic, and planning the digest for a peptide-mapping or MAM method — the trypsin list is the peptide map you will get.

Returns the same protease analysis that covabio_peptide embeds, on its own and for any protein length.

Parameters:
  sequence: Amino acid sequence.

Returns: {sites: {trypsin, chymotrypsin, pepsin, elastase}, total_cleavage_sites, stability_score, classification}

Input Schema

Name	Required	Description	Default
`api_key`	No
`sequence`	Yes

Output Schema

Name	Required	Description	Default
`result`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 9, 2026

TDQS

A4.1/5.0

Behavior4/5

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

With no annotations, the description carries the behavioral burden and does well: it discloses the exact cleavage rules per protease (e.g. trypsin after K/R but not before P) and the shape of the output (per-protease position lists, total count, 0-100 score, three-way classification). It omits error/edge behavior and any auth or rate-limit context.

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-loaded with purpose and rules, then use cases, then output shape. Dense but every sentence carries information; the protease rule list is compact rather than padded.

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?

For a no-annotation, single-input analysis tool the description is largely self-sufficient: rules, scoring scale, classifications, and return fields are all stated (and the output schema independently documents the return shape). Minor gaps are input format expectations and failure conditions.

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 0%, so the description must compensate. It labels 'sequence' as an amino acid sequence and 'for any protein length' implies no length cap, which is useful, but it adds no format detail (one-letter code, allowed characters) and never mentions the second parameter, api_key.

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+resource ('Map protease cleavage sites and score proteolytic stability') and enumerates the exact proteases and their rules. It also differentiates from the sibling covabio_peptide by noting it returns the same analysis standalone and for any protein length.

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

Usage Guidelines4/5

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

Explicitly names two use cases (in-vivo half-life/serum stability prediction and peptide-mapping/MAM digest planning) and clarifies the relationship to covabio_peptide. It gives clear routing context but does not state when the embedding tool would be preferable instead.

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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