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Agent skill

Struct Predictor

by majiayu000 in majiayu000/claude-skill-registry

Local protein structure prediction with AlphaFold, Boltz, or Chai.

MITAuto-check passedResearch & Science

Install Struct Predictor

skills CLI
$ npx skills add majiayu000/claude-skill-registry --skill struct-predictor -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install majiayu000/claude-skill-registry struct-predictor --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/majiayu000/claude-skill-registry.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/ai-ml/struct-predictor .claude/skills/struct-predictor && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
struct-predictor
GitHub stars
666
Used in
2 other repos
Token cost
~406 tokens
SKILL.md length
139 words
Files
2
Skills in repo
1,273
Repo updated
First seen
Licence
MIT

At a glance

Local protein structure prediction with AlphaFold, Boltz, or Chai.

  • Works in 5 steps: Structure Prediction: Run AlphaFold… → PDB Retrieval: Fetch experimental… → Structure Comparison: Compute RMSD,… → …
  • Tasks that involve Protein structure and design
  • SKILL.md covers Core Capabilities, Dependencies, Example Queries and Status
  • Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Struct Predictor is an agent skill from majiayu000/claude-skill-registry. Local protein structure prediction with AlphaFold, Boltz, or Chai. Compare predicted structures, compute RMSD, visualise 3D models.

Its SKILL.md is about 410 tokens, which your agent loads only when the skill is triggered. The skill folder holds 1 other file (for example `metadata.json`).

It sits in Research & Science, covering Protein structure and design and 3D graphics and WebGL. It works with AlphaFold. The repository describes itself as: Searchable Claude Code skills catalog with source-linked guides and generated registry artifacts. The licence is MIT.

When your agent uses it

  • Tasks that involve Protein structure and design
  • Tasks that involve 3D graphics and WebGL

Example prompts

  • “/struct-predictor”

Requirements

  • Python 3

Workflow steps

5 steps, taken from the first numbered list in SKILL.md.

  1. Structure Prediction: Run AlphaFold (ColabFold), Boltz-1, or Chai locally
  2. PDB Retrieval: Fetch experimental structures from PDB via OpenBio
  3. Structure Comparison: Compute RMSD, TM-score between predicted and reference structures
  4. Confidence Mapping: Visualise pLDDT and PAE confidence metrics
  5. Report Generation: Markdown with 3D renders, confidence plots, and comparison tables

What it can do on your machine

Read from SKILL.md and the folder at commit 2d14a69. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    No scripts in the folder and no shell commands in SKILL.md.

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Struct Predictor loads about 406 tokens when it runs. Until then it costs about 37 tokens; SKILL.md has 139 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~37
When it runs · the whole SKILL.md, loaded when a task matches
~406

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from majiayu000/claude-skill-registry at commit 2d14a69, republished under its MIT licence (© majiayu000). 139 words, ~406 tokens.

Download SKILL.mdSave it as .claude/skills/struct-predictor/SKILL.md (or your agent's skills folder). This skill also uses 1 other file; get the full folder from GitHub.
name
struct-predictor
description
Local protein structure prediction with AlphaFold, Boltz, or Chai. Compare predicted structures, compute RMSD, visualise 3D models.
version
0.1.0

Struct Predictor

You are the Struct Predictor, a specialised agent for protein structure prediction and analysis.

Core Capabilities

  1. Structure Prediction: Run AlphaFold (ColabFold), Boltz-1, or Chai locally
  2. PDB Retrieval: Fetch experimental structures from PDB via OpenBio
  3. Structure Comparison: Compute RMSD, TM-score between predicted and reference structures
  4. Confidence Mapping: Visualise pLDDT and PAE confidence metrics
  5. Report Generation: Markdown with 3D renders, confidence plots, and comparison tables

Dependencies

  • colabfold_batch or boltz or chai (at least one local predictor)
  • biopython (PDB parsing)
  • Optional: pymol (3D rendering), py3Dmol (interactive visualisation)

Example Queries

  • "Predict the structure of this protein sequence: MKWVTF..."
  • "Compare AlphaFold prediction of BRCA1 to the experimental PDB structure"
  • "Show the pLDDT confidence plot for my predicted structure"
  • "What is the RMSD between these two PDB files?"

Status

Planned -- implementation targeting Week 4-5 (Mar 20 - Apr 2).

© majiayu000, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 1 other file in skills/ai-ml/struct-predictor of majiayu000/claude-skill-registry.

  • SKILL.md
  • metadata.json

Open the folder on GitHubat commit 2d14a69

Used in 2 other repositories

We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 2 other GitHub owners. This page covers the copy in majiayu000/claude-skill-registry, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Struct Predictor next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Struct Predictor compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Struct Predictor this skillmajiayu000/claude-skill-registry6662 repos~406Automated safety check: PassMIT
Alphafold Database Fetch And Analyzegoogle-deepmind/science-skills3.2k2 repos~1.2kAutomated safety check: PassApache-2.0
Alphafoldadaptyvbio/protein-design-skills1634 repos~1.2kAutomated safety check: PassMIT
Chaiadaptyvbio/protein-design-skills1634 repos~1.5kAutomated safety check: PassMIT
Biopipelineslocbp-uzh/biopipelines109—~2.4kAutomated safety check: PassMIT
Rfdiffusionadaptyvbio/protein-design-skills1634 repos~2.3kAutomated safety check: PassMIT

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Works with

Categories

Questions about Struct Predictor

What does Struct Predictor do?

Local protein structure prediction with AlphaFold, Boltz, or Chai. Struct Predictor is an agent skill from majiayu000/claude-skill-registry. Local protein structure prediction with AlphaFold, Boltz, or Chai.

When should I use Struct Predictor?

Struct Predictor fits situations like: tasks that involve Protein structure and design; tasks that involve 3D graphics and WebGL.

How do I install Struct Predictor in Claude Code?

Run `npx skills add majiayu000/claude-skill-registry --skill struct-predictor -a claude-code`. Or copy the skill folder (skills/ai-ml/struct-predictor in majiayu000/claude-skill-registry) into .claude/skills/struct-predictor in your project. Claude Code loads it when a task matches its description.

How do I install Struct Predictor in Codex?

Run `npx skills add majiayu000/claude-skill-registry --skill struct-predictor -a codex`. Or copy the skill folder (skills/ai-ml/struct-predictor in majiayu000/claude-skill-registry) into .agents/skills/struct-predictor in your project. Codex loads it when a task matches its description.

Can I use Struct Predictor in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add majiayu000/claude-skill-registry --skill struct-predictor -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/struct-predictor, .gemini/skills/struct-predictor, .github/skills/struct-predictor and .opencode/skills/struct-predictor in your project.

What does Struct Predictor need to run?

SKILL.md names no scripts, command-line tools or credentials: Struct Predictor is instructions for the agent only. Our summary lists: Python 3.

Does Struct Predictor access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Struct Predictor safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Struct Predictor use?

Struct Predictor is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Struct Predictor use?

About 406 tokens (SKILL.md is roughly 1.6k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Struct Predictor?

Skills that share tags, products or a category with Struct Predictor: Alphafold Database Fetch And Analyze (google-deepmind/science-skills, 3.2k stars), Alphafold (adaptyvbio/protein-design-skills, 163 stars), Chai (adaptyvbio/protein-design-skills, 163 stars) and Biopipelines (locbp-uzh/biopipelines, 109 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Struct Predictor?

majiayu000 (a GitHub user) maintains it in majiayu000/claude-skill-registry, which has 666 GitHub stars. The repository holds 1,273 skills in this directory. The repository was last updated on October 7, 2026.

Source: majiayu000/claude-skill-registry on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.