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How to fold a protein in a free Colab notebook with Colab Fold

Open the AlphaFold2_mmseqs2 notebook, paste a sequence and get a predicted structure without installing anything.

Short answer: Open the AlphaFold2_mmseqs2 notebook from the table in the README (monomers and complexes, MMseqs2 MSAs, templates); then paste your sequence and run the cells; use ESMFold or the AlphaFold3 (OpenFold3) notebook if you want to compare; download the predicted structure files when the run finishes. All steps.

Who it is forA biology student or wet-lab researcher who needs a structure model for one protein or complex today.

The problemRunning AlphaFold locally needs big databases, a GPU and setup time most people do not have.

The outcomeA predicted structure with pLDDT confidence values, from a notebook in your browser.

What you need first

  • A Google account for the Colab notebooks, or a local ColabFold install for colabfold_search and colabfold_batch
  • For local searches: MMseqs2 and the ColabFold databases (large downloads, a lot of CPU)
  • A GPU for structure prediction; about 16 GB of GPU memory handles sequences up to roughly 2000 residues
  • For GPU search: GPU databases set up with GPU=1

Steps

  1. Open the AlphaFold2_mmseqs2 notebook from the table in the README (monomers and complexes, MMseqs2 MSAs, templates)
  2. Paste your sequence and run the cells; use ESMFold or the AlphaFold3 (OpenFold3) notebook if you want to compare
  3. Download the predicted structure files when the run finishes
  4. Color by pLDDT in PyMOL with spectrum b, red_yellow_green_cyan_blue, minimum=50, maximum=90
  5. For molecular replacement, remember the bfactor column holds pLDDT (higher is better), not a real B-factor

Prompt for your agent

I want to use sokrypton/ColabFold's AlphaFold2_mmseqs2 notebook for this sequence: <sequence>. Walk me through the settings to choose, then explain how to read the pLDDT values in the result.

Caveat. Maximum length depends on the free GPU Google Colab gives you; the README suggests about 2000 residues on 16 GB GPUs.

Use this in your AI agent

Ask your agent

Using the Deduped MCP, get the setup steps for sokrypton/ColabFold and "Fold a protein in a free Colab notebook"

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claude mcp add --transport http deduped https://dedupedai.com/mcp

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