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AlphaFold Protein Structure Validation

A skill for validating designed protein sequences and binder–target complexes with AlphaFold2/ColabFold and interpreting confidence metrics.

Data & AnalyticsAdvanced★ 191⑂ 33AI score 9/10Last updated: Jul 1, 2026

What it does

  • Predicts whether designed sequences fold as intended using AlphaFold2.
  • Predicts multi-chain binder–target complexes with ColabFold / AlphaFold-Multimer.
  • Extracts and interprets confidence metrics (pLDDT, pTM, ipTM, PAE) against pass thresholds: pLDDT > 85, pTM > 0.70, ipTM > 0.50, interface PAE < 10.
  • Provides a decision tree for choosing local install vs. ColabFold vs. Modal GPU, runtime/cost estimates per campaign size, and an error→fix table (CUDA OOM, missing MSA databases, timeouts).

Who it's for

  • Computational biologists doing protein design and binder screening.
  • Teams needing self-consistency validation of de novo designs.
  • Anyone batch-predicting hundreds to thousands of sequences on cloud GPUs (Modal).

Example uses

  1. "Run these 100 binder sequences through ColabFold multimer and keep only hits with ipTM > 0.5."
  2. "Parse result_model_1.pkl and summarize mean pLDDT and interface PAE in a table."
  3. "I hit CUDA out of memory — what now?" → switch to A100 or use ColabFold's MSA server.

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/BioTender-max/awesome-bio-agent-skills/HEAD/skills/adaptyv/alphafold/SKILL.md

What I want: (describe your task here)

If Claude can't open the link, open it yourself and paste the contents instead.

↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on Claude Skill Mart.
Copy the skills/adaptyv/alphafold folder from the GitHub repo BioTender-max/awesome-bio-agent-skills into my ~/.claude/skills/alphafold/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/BioTender-max/awesome-bio-agent-skills.git && mkdir -p ~/.claude/skills && cp -r awesome-bio-agent-skills/skills/adaptyv/alphafold ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Clone the skills repository: git clone https://github.com/BioTender-max/awesome-bio-agent-skills.git
  2. Create the skills folder: mkdir -p ~/.claude/skills
  3. Copy just this skill: cp -r awesome-bio-agent-skills/skills/adaptyv/alphafold ~/.claude/skills/
  4. Restart Claude Code and test with a prompt like "use the alphafold skill to validate this sequence."
  5. For real runs, prepare the environment: Python 3.10+, CUDA 11+, a 32GB+ GPU (A100 recommended), a Modal account, and the biomodals repo (for modal run modal_colabfold.py).
  6. For local execution, git clone https://github.com/deepmind/alphafold.git and download the MSA databases (hundreds of GB). If disk is limited, prefer ColabFold's hosted MSA server.
View source on GitHub ↗License: NOASSERTION