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Jean — Molecular Biology & Genomics

antibody_molecule

Read-only

Properties of an assembled antibody from its heavy and light chains: molecular weight, isoelectric point, net charge at a pH, and the extinction coefficient and A280 with cysteines reduced and with every pair formed into a cystine, for a Fab (1 heavy + 1 light) or an IgG (2 + 2).

Input Schema

NameRequiredDescriptionDefault
pHNothe pH the net charge is reported at.
heavyYesthe heavy chain (one-letter amino acids), as much of it as the molecule carries.
lightYesthe light chain (kappa or lambda, one-letter amino acids).
_filesNoThe project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
formatNohow many copies of each chain the molecule holds. Values: fab (Fab (1 heavy + 1 light)), igg (IgG (2 heavy + 2 light)).igg
_subjectNoThe record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.

Output Schema

NameRequiredDescriptionDefault
absorbanceYesA280 of a 1 g/L solution, `reduced` and `cystines`
chargeAtPHYesnet charge at the requested pH
extinctionYesε280 in M⁻¹ cm⁻¹, `reduced` and `cystines`
molecularWeightYesaverage mass of the whole molecule, Da (chains reduced)
isoelectricPointYesisoelectric point of the whole molecule (Bjellqvist pKs, each chain with its own termini)

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A3.9/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false, and openWorldHint=false, so the safety profile is covered. The description adds substantive computational behavior beyond annotations: it computes extinction coefficient and A280 both with cysteines reduced and with every pair formed into a cystine, and it ties results to Fab versus IgG stoichiometry.

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?

It is a single dense sentence that front-loads the outputs and then the chain stoichiometry. Every clause contributes, though the long enumerated list is slightly run-on compared with a more structured presentation.

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?

With an output schema present and full parameter documentation, the description covers what is computed and the key cysteine-state distinction. It does not discuss validation or error behavior, but those gaps are minor for a read-only calculation tool.

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 100%, so the schema already documents heavy, light, pH, and format. The description reinforces the format stoichiometry and the pH role for net charge, but mostly restates the schema rather than adding new semantic detail.

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 names a very specific resource and computation: assembled antibody properties (molecular weight, isoelectric point, net charge at pH, extinction coefficient, A280) from heavy and light chains. The explicit Fab/IgG stoichiometry distinguishes it from generic protein-property siblings like protein_properties.

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 antibody-assembly framing and the Fab/IgG formats, but there is no explicit when-to-use guidance, no prerequisites, and no routing to alternatives such as protein_properties or compare_antibodies.

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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