AlterLab AlphaFold (via ColabFold)
Runs AlphaFold2 via ColabFold to fold proteins/complexes and interpret pLDDT/pTM/ipTM/PAE confidence.
Test report
- Verdict
- Works with setup
- Score
- Tested
- Jul 14, 2026
- Environment
- Claude Code 2.x (agent harness)
- Upstream re-checked
- Aug 10, 2026 · 18ca146
Correctly routes a ProteinMPNN-designed peptide into the self-consistency fold-and-check loop and hands the GPU step off to alterlab-remote-compute -- but actual folding needs a CUDA GPU plus multi-GB AlphaFold2 weights that this sandbox doesn't have, so only the guidance layer could be verified.
Scored on four weighted criteria — install, triggering, output vs. baseline, docs. How scoring works
- Installs cleanly 5/5
- Triggers reliably 5/5
- Output vs. baseline 7/10
- Docs & honesty 5/5
What AlterLab AlphaFold (via ColabFold) does
Predicts 3D protein structures from a FASTA sequence using AlphaFold2 through ColabFold's MMseqs2-accelerated MSA pipeline, covering single-chain monomers and AlphaFold2-Multimer complexes. Explains how to read per-residue and per-interface confidence metrics and how to validate a designed sequence via self-consistency refolding. Part of a larger AlterLab suite; explicitly defers to sibling skills for ligand co-folding, antibody complexes, embeddings, or database lookups. Requires a CUDA GPU and ColabFold install.
How to install AlterLab AlphaFold (via ColabFold)
git clone https://github.com/AlterLab-IEU/AlterLab-Academic-Skills
cd AlterLab-Academic-Skills
mkdir -p ~/.claude/skills
cp -r skills/bioinformatics/alterlab-alphafold ~/.claude/skills/alterlab-alphafold
Skills live in ~/.claude/skills/ (global) or .claude/skills/
(per-project). Restart Claude Code after installing.
Commands — how to trigger AlterLab AlphaFold (via ColabFold)
-
/alterlab-alphafoldRuns AlphaFold2 via ColabFold to fold proteins/complexes and interpret pLDDT/pTM/ipTM/PAE confidence.
It also activates on plain-language prompts like these:
-
Fold this FASTA sequence and give me pLDDT confidence scores. -
Predict this protein complex structure with AlphaFold2-Multimer. -
I designed this peptide with ProteinMPNN, check if it folds back.
Frequently asked questions
- Is the AlterLab AlphaFold (via ColabFold) skill free?
- Yes. The skill itself is free from AlterLab-IEU/AlterLab-Academic-Skills. SkillProof publishes the install command and an independent test verdict at no cost.
- Does AlterLab AlphaFold (via ColabFold) work with Claude Code?
- We tested it with Claude Code 2.x (agent harness) on Jul 14, 2026. Verdict: Works with setup. Correctly routes a ProteinMPNN-designed peptide into the self-consistency fold-and-check loop and hands the GPU step off to alterlab-remote-compute -- but actual folding needs a CUDA GPU plus multi-GB AlphaFold2 weights that this sandbox doesn't have, so only the guidance layer could be verified.
- What is the AlterLab AlphaFold (via ColabFold) SkillProof Score?
- 8.8/10 — installs cleanly 5/5, triggers reliably 5/5, output vs. baseline 7/10, docs & honesty 5/5.
- How do I install AlterLab AlphaFold (via ColabFold)?
- Copy the install command from this page, run it in your terminal, and restart Claude Code. Skills live in ~/.claude/skills/ (global) or .claude/skills/ inside a project.
- Can I use AlterLab AlphaFold (via ColabFold) with Cursor, Copilot, Gemini CLI, Codex or other AI tools?
- The SKILL.md format is native to Claude (Claude Code, Desktop, claude.ai). The instructions inside adapt to other assistants: Cursor rules, GitHub Copilot instructions, Windsurf rules, Custom GPTs, AGENTS.md for OpenAI Codex, and GEMINI.md for Google Gemini CLI — our conversion guides cover each, and the free converter on the tools page does the wrapping for you.