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CovaSyn Chemistry Tools

covabio_antibody

Identify CDR regions (complementarity-determining regions) and framework regions in an antibody sequence. Supports Kabat, Chothia, and IMGT numbering schemes. Returns CDR boundaries, chain type (heavy/light), framework sequences, and CDR developability flags.

Parameters:
  sequence: Antibody heavy or light chain amino acid sequence.
  scheme: Numbering scheme — "kabat" (default), "chothia", or "imgt".

Returns: {chain_type, CDR1/2/3 sequences and positions, framework_regions, cdr_developability}

Input Schema

NameRequiredDescriptionDefault
schemeNokabat
api_keyNo
sequenceYes

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A3.7/5.0
Behavior3/5

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

No annotations are provided, so the description carries the disclosure burden. It usefully states the return fields (chain type, CDR boundaries, frameworks, developability flags) and numbering schemes, but does not address permissions, API-key requirements, error behavior, or explicitly confirm that the operation is read-only.

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, then parameters and returns. The parameter/return recap is somewhat redundant with the schema and output schema, but it is controlled and useful given 0% schema description coverage.

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?

Output schema exists, so return details are optional; the description still summarizes them. It covers the main input semantics and behavior sufficiently for an agent to invoke the tool, though the unexplained api_key parameter and lack of usage alternatives leave a small gap.

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 must compensate. It defines sequence as an antibody heavy/light amino acid sequence and enumerates scheme values (kabat default, chothia, imgt), which is valuable; however, it omits the api_key parameter entirely.

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?

Specific verb and resource: identifies CDR and framework regions in an antibody sequence, and names supported numbering schemes. This distinguishes it from siblings such as covabio_developability, covabio_sequence_utils, and covabio_protein_profile, which do not perform antibody numbering.

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?

Usage is implied by the purpose (use on an antibody heavy/light chain sequence when CDR/framework annotation is needed) and by the scheme parameter options. However, it gives no explicit when-to-use guidance, no exclusions, and does not name a sibling alternative for related tasks.

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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