Interface Analysis (bioSkills)

A Claude Code skill that maps protein–protein and protein–ligand interfaces: which residues are in contact, how much surface each partner buries, and whether the interface is biological or a crystallization artifact.


Type	Claude Skill
Supplier	GPTomics bioSkills (community OSS, MIT)
Availability	GA — part of the bioSkills collection
Pricing	Free / OSS (MIT) — Biopython, NumPy and the optional FreeSASA are separately installed OSS; PDBePISA is a free EBI web service
Capabilities	Read/Write — Claude runs the skill’s workflow locally (Bash/Python), not as an MCP tool
Verified	works · 2026-08-03
Security	cleared · 2026-08-03 — GPTomics/bioSkills MIT confirmed, provenance matches, no advisories

How to install

bioSkills is not an npm package — skills are plain markdown/code read directly by the agent. Clone the repo, then either run the installer for the whole category or copy the single skill directory.

Claude Code — clone and install via the bundled script:
```
git clone https://github.com/GPTomics/bioSkills
cd bioSkills
./install-claude.sh --categories "structural-biology"
```
The installer copies matching skills into ~/.claude/skills/ (default target). Use ./install-claude.sh --list to preview the skills first.
Claude Code / other agents — copy just this one skill:
```
cp -r bioSkills/structural-biology/interface-analysis ~/.claude/skills/
```
(run from inside your clone — the previous step left you in bioSkills/; otherwise replace bioSkills/ with the absolute path of your clone).

What it does

Walks the interface calculation while forcing the two decisions people usually skip — which cutoff, and which assembly:

Cutoff choice, stated explicitly — heavy-atom 4–5 Å for van der Waals contact, Cα–Cα 8 Å for a topological definition, 3.5–4.0 Å for hydrogen bonds and salt bridges. The skill requires the rationale to be recorded, because the residue list changes with the cutoff.
Contacts — NeighborSearch over non-hydrogen atoms, collecting cross-chain pairs.
Buried surface area — a contact list is not an interface: SASA is computed with ShrakeRupley on the complex and on each isolated chain at an identical probe radius (1.4 Å default), then BSA = SASA(A) + SASA(B) − SASA(complex), halved for per-partner area. FreeSASA 2.2+ is an optional Lee–Richards alternative.
Biology vs crystal packing — cross-checks BSA magnitude, hydrogen bonding, interface conservation and the PDBePISA complexation-significance score, and pushes for corroboration from solution data before calling an interface real.
Assembly discipline — computes on the biological assembly, not the asymmetric unit, which is the single most common source of spurious interfaces.
Applications — ligand-contact residues and antibody/antigen epitope residues fall out of the same contact machinery.
Components — Bio.PDB (primary), Biopython 1.83+, NumPy 1.26+, FreeSASA 2.2+ (optional), PDBePISA (external web service, no local binding).

Primary use cases: protein–protein interface mapping, epitope residue identification, ligand contact footprints, screening out crystal-packing contacts.

Notes

Distributed as a SKILL.md (plus reference material) in the bioSkills collection — Claude executes the workflow locally rather than as an MCP server. The upstream skill front-matter name is bio-structural-biology-interface-analysis; if invoked as a namespaced plugin command it resolves under the bioSkills plugin, not as a bare /interface-analysis. PDBePISA has no local Python binding — its complexation-significance score is read from the web service, so that step is manual or scripted against the EBI endpoint. Complements the catalogued PDBe and RCSB PDB entries for fetching biological assemblies, Complex Portal and IntAct for orthogonal interaction evidence, and the Epitope Prediction skill for the immunology case. Upstream directory: structural-biology/interface-analysis.

Sources

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