Structure Preparation (bioSkills)

A Claude Code skill that turns a deposited or predicted structure into one you can actually dock, simulate, or run electrostatics on — adding hydrogens, assigning protonation and tautomer states, and filling in what the experiment never resolved.


Type	Claude Skill
Supplier	GPTomics bioSkills (community OSS, MIT)
Availability	GA — part of the bioSkills collection
Pricing	Free / OSS (MIT) — PDBFixer, OpenMM, PROPKA 3 and PDB2PQR are separately installed OSS; `reduce`/Reduce2 ships with CCTBX/Phenix (free for academic use under its own licence)
Capabilities	Read/Write — Claude runs the skill’s workflow locally (Bash/Python) and writes prepared structure files, not as an MCP tool
Verified	works · 2026-08-06
Security	caution · 2026-08-06 — GPTomics/bioSkills MIT, but bundled reduce/Reduce2 ships with Phenix, academic-use-only licence

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/structure-preparation ~/.claude/skills/
```
(run from inside your clone — the previous step left you in bioSkills/; otherwise replace bioSkills/ with the absolute path of your clone). The skill checks its own dependencies with pip show <package> and <tool> --version before running.

What it does

Runs the preparation sequence and — the part that matters downstream — records what was built rather than observed:

Hydrogens — adds the hydrogens an X-ray model never resolved, with reduce/Reduce2 for optimized placement.
Protonation and tautomers — assigns His HID/HIE/HIP tautomers, Asn/Gln/His 180° flips, and pKa-shifted Cys/Lys/Asp/Glu states at a stated pH and local microenvironment using PROPKA 3, instead of assuming standard pKa values at pH 7.
Missing atoms and loops — finds gaps by comparing SEQRES to modelled atoms, replaces nonstandard residues (MSE, PTR, other modified forms) with their standard parents, fills missing side-chain atoms, and models short missing loops explicitly as disorder hypotheses rather than as data.
Predicted models — the prep path for an AlphaFold/ESMFold model after low-pLDDT regions have been trimmed.
Electrostatics output — writes a PQR file with PDB2PQR 3.0 for Poisson–Boltzmann calculations.
Components — PDBFixer 1.9+ (primary), OpenMM 8.1+, plus the separately installed CLI tools reduce/Reduce2, PROPKA 3 and PDB2PQR 3.0 (conda-forge or pip).

Primary use cases: docking receptor prep, MD system setup, Poisson–Boltzmann electrostatics input, cleaning up a predicted model.

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-structure-preparation; if invoked as a namespaced plugin command it resolves under the bioSkills plugin, not as a bare /structure-preparation. The three CLI dependencies are not installed by the skill and are the usual friction point — reduce in particular normally arrives via a CCTBX or Phenix installation rather than pip. Sits between the catalogued Structure Validation skill (decide whether the model is usable, trim low-pLDDT regions) and the downstream simulation and docking entries OpenMM MCP Server, GROMACS MCP Server, AutoDock Vina and smina. Upstream directory: structural-biology/structure-preparation.

Sources

Installed this tool?

Share feedback — install path, OS, errors, workarounds. The form opens with this tool pre-selected and a link back to this page.