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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). Each chain keeps its own termini, so this is not the same as pasting the chains end to end. Graded against Biopython ProtParam over every heavy/light pair of ANARCI's PDB benchmark.

Input Schema

TableJSON 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

TableJSON 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

A3.8/5.0
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 clear. The description adds useful behavioral detail: it computes MW, pI, pH-dependent net charge, extinction coefficient, and A280 under reduced and cystine-paired cysteine states, and it discloses the chain-termini handling and benchmark validation.

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?

The description is three dense sentences, front-loaded with the computed properties and format distinction. The final benchmark sentence is somewhat ancillary but supports trustworthiness, and every sentence contributes without excessive 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?

An output schema exists, so return values need not be exhaustively described, and annotations cover safety and world scope. The description nonetheless supplies enough context about antibody assembly, Fab/IgG formats, cysteine treatment, and termini handling for correct invocation, leaving only sibling-choice guidance as a minor gap.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100%, so the schema already documents pH, heavy, light, format, _files, and _subject. The description adds meaning beyond the schema by clarifying that heavy and light chains are assembled as a molecule rather than concatenated, and by explaining the Fab versus IgG copy-number distinction in terms of assembled antibody structure.

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?

The description states a specific resource and computed outputs: properties of an assembled antibody from heavy and light chains, including MW, pI, net charge, extinction coefficient, and A280 for Fab or IgG. It is clearly distinct from generic protein_properties because it specifies antibody assembly, but it does not explicitly name or compare against any sibling tool.

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 description: use it to compute molecular properties for an assembled Fab or IgG from separate heavy and light chains. The caveat that chains keep their own termini hints at correct versus incorrect usage, but there is no explicit when-to-use guidance or comparison with alternatives such as protein_properties or antibody_isotype.

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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