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How to predict an all atom structure from a sequence with Esm

Run ESMFold2 locally to fold a protein, including DNA chains and ligands, and write the result as mmCIF.

Short answer: Install the package with pip install esm; then build a StructurePredictionInput with ProteinInput, DNAInput and LigandInput entries as in the README example; load the model with EsmFold2Model.from_pretrained and call ESMFold2InputBuilder().fold with num_loops, num_sampling_steps and a seed. All steps.

platform. AMD ROCm users need ROCm 6.4 or newer, and Esm requires PyTorch 2.11.

Who it is forA structural biologist who wants a predicted complex without a cluster job.

The problemStructure prediction pipelines are hard to assemble and slow to run.

The outcomeA .cif file of the predicted complex plus pLDDT, pTM and ipTM scores.

What you need first

  • Python with pip; `pip install esm` is about 5.6 GB, of which about 4.6 GB is the CUDA build of torch
  • A CUDA GPU for the local examples, which load models with device set to cuda
  • A Biohub Platform API token if you use the hosted client instead of local weights

Steps

  1. Install the package with pip install esm
  2. Build a StructurePredictionInput with ProteinInput, DNAInput and LigandInput entries as in the README example
  3. Load the model with EsmFold2Model.from_pretrained and call ESMFold2InputBuilder().fold with num_loops, num_sampling_steps and a seed
  4. Print result.plddt, result.ptm and result.iptm, then write result.complex.to_mmcif() to a .cif file

Prompt for your agent

With Biohub/esm, fold <my protein sequence> with ESMFold2 using ESMFold2InputBuilder().fold, print pLDDT, pTM and ipTM, and save the structure as a mmCIF file I can open in a viewer.

Caveat. The README notes the model is validated for protein protein interaction design; treat any prediction as a hypothesis to test.

Use this in your AI agent

Ask your agent

Using the Deduped MCP, get the setup steps for Biohub/esm and "Predict an all atom structure from a sequence"

Add Deduped to Claude Code once

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

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