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CovaSyn Chemistry Tools

covabio_protein_profile

Compute 30+ biophysical properties of a protein from its amino acid sequence. Returns molecular weight, isoelectric point, extinction coefficient, GRAVY (hydrophobicity), instability index, aromaticity, charge profile across pH range, amino acid composition, and secondary structure fractions.

Parameters:
  sequence: Amino acid sequence (1-letter code, e.g. "MKWVTFISLLLLFSSAYS...").

Returns: {molecular_weight, isoelectric_point, gravy, instability_index, charge_profile, ...}

Input Schema

NameRequiredDescriptionDefault
api_keyNo
sequenceYes

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

B3.2/5.0
Behavior3/5

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

No annotations are provided, so the description carries the full behavioral burden. It discloses the outputs and that it is a pure computation, but says nothing about whether an api_key is required, authentication, cost/rate limits, or failure behavior on invalid sequences.

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 the core purpose and efficiently enumerates outputs. The trailing 'Returns: {...}' line is somewhat redundant since an output schema already exists, but overall it is tight and well-structured.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

An output schema exists, so the return-value listings are more than needed, yet the description omits the api_key prerequisite and any auth/cost context for a tool with no annotations. Adequate but with clear gaps for correct invocation.

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%. The description compensates well for the 'sequence' parameter (1-letter code plus a concrete example), which the schema lacks, but the second parameter 'api_key' is undocumented in both schema and description. Net effect is partial compensation for a 2-param tool.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb+resource ('Compute 30+ biophysical properties of a protein from its amino acid sequence') and enumerates the concrete outputs, so an agent knows exactly what it produces. It does not distinguish itself from overlapping siblings like covabio_charge_profile or covabio_batch_profile, which also cover some of the same properties.

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

Usage Guidelines2/5

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

There is no when-to-use or when-not-to-use guidance, and no alternatives are named despite several sibling tools (covabio_charge_profile, covabio_developability, covabio_batch_profile) that clearly overlap. The agent is left to infer the selection criteria entirely.

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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