jean — Molecular Biology & Genomics

antibody_antigen_contacts

Read-only

Type the ANTIBODY-ANTIGEN INTERFACE of a deposited complex: which residue of each antibody chain touches which residue of the antigen, how close, and what kind of interaction each pair makes - ionic, polar, weak polar, hydrophobic, aromatic, carbonyl, or a disulfide. The antigen is found rather than named: a protein chain with no immunoglobulin variable domain is the thing being bound. Geometric definitions are CREDO's as Arpeggio implements them, graded contact-for-contact against pdbe-arpeggio. polar is the hydrogen-bond criterion WITHOUT the donor angle, because a crystal structure carries no hydrogens; it is the superset an angle test would filter, and no angle-checked hydrogen bond is claimed.

Input Schema

TableJSON Schema

Name	Required	Description
`text`	Yes	the coordinate file's contents - a PDB flat file or a PDBx/mmCIF; the format is read from the bytes, not from a name.
`model`	No	which model of an ensemble to type, 1-based: conformers touch in different places, so one is typed rather than all.
`_files`	No	The 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.
`_subject`	No	The 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.
`antibodyChain`	No	type only this chain against the antigen. Left out, every chain carrying a variable domain is typed.
`antigenChains`	No	comma-separated chain ids to treat as the antigen. Left out, every protein chain with no variable domain is the antigen.
`interactingCutoff`	No	atom pairs further apart than this (Å) are not reported at all; Arpeggio's own default is 5.

Output Schema

TableJSON Schema

Name	Required	Description
`byType`	Yes	atom pairs carrying each type over the whole interface, distance bands included
`contacts`	Yes	one row per residue pair: the antibody residue (chain, author number, name, and its scheme position where it sits in a variable domain), the antigen residue, the closest atom distance, the atom-pair count, and the interaction types
`residues`	Yes	how many residues each side contributes, per antibody chain
`antigenChains`	Yes	the chain ids treated as the antigen
`antibodyChains`	Yes	the chains typed, each with its variable-domain chain types

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 20, 2026

TDQS

A4.4/5.0

Behavior5/5

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

Annotations already declare readOnlyHint, destructiveHint false, and openWorldHint false, but the description adds substantial behavioural context beyond them. It discloses the interaction classes reported, the geometric definitions used (CREDO's as Arpeggio implements them), and an important limitation: `polar` is a hydrogen-bond criterion without the donor angle because crystal structures carry no hydrogens, so no angle-checked hydrogen bond is claimed.

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 front-loaded with the primary purpose and then adds necessary caveats, with no obvious filler. It is longer and denser than most definitions, but every sentence contributes to understanding the tool's scope or its geometric/chemical contract.

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

Completeness5/5

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

Given the rich schema coverage, read-only annotations, and an output schema, the description is complete enough for an agent to invoke the tool correctly. It covers purpose, antigen-detection behaviour, interaction semantics, and the key limitation of the polar criterion without needing to duplicate return-value documentation.

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 parameter definitions already carry the semantic load. The description adds conceptual context about antigen discovery and the `polar` interaction type, but does not give additional parameter-specific syntax, format, or edge-case guidance beyond what the schema provides.

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 ('Type') and resource ('ANTIBODY-ANTIGEN INTERFACE of a deposited complex'), and enumerates exactly what is reported: which residues touch, how close, and the interaction type. An agent can distinguish this from neighbouring antibody tools such as antibody_liabilities, antibody_isotype, or graft_antibody_cdrs without opening any schema.

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?

The description gives clear context for use: a deposited complex is required, and the antigen is found rather than named, with the rule that chains lacking an immunoglobulin variable domain are treated as antigen. It does not explicitly name alternative tools or state when not to use this one, so it falls short of the top mark.

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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