DEDUPED Hot AI repos. Real use cases. What people build. Get the Monday 5

How to predict a protein complex structure with Boltz with Boltz

Describe your biomolecules in a YAML file and let Boltz predict the structure of the complex.

Short answer: Create a fresh Python environment, as the README recommends; then install with pip install boltz[cuda] -U (drop [cuda] on CPU-only or non-CUDA GPU hardware); write an input YAML file describing the biomolecules you want to model, following docs/prediction.md. All steps.

  • Top pick
  • Security and science
  • Intermediate
  • 1 hour
  • From the README
  • Claude Code
  • Codex
  • Cursor
  • Gemini CLI

platform. The CPU version is significantly slower than the GPU version, so large complexes realistically need an NVIDIA GPU.

Who it is forA structural biologist who wants a quick open-source structure model of a complex before setting up experiments.

The problemGetting a structure prediction for a complex usually means a hosted service, a queue or a closed model.

The outcomePredicted complex structures written by the latest Boltz model on your own machine.

What you need first

  • Python in a fresh environment and pip
  • An NVIDIA GPU for the [cuda] install; CPU-only works but is significantly slower
  • Input YAML files describing the biomolecules (format in docs/prediction.md)
  • Network access for the optional MSA server (--use_msa_server)

Steps

  1. Create a fresh Python environment, as the README recommends
  2. Install with pip install boltz[cuda] -U (drop [cuda] on CPU-only or non-CUDA GPU hardware)
  3. Write an input YAML file describing the biomolecules you want to model, following docs/prediction.md
  4. Run boltz predict input_path --use_msa_server with input_path pointing at the YAML file
  5. Check every option with boltz predict --help

Prompt for your agent

Using jwohlwend/boltz, install it in a fresh environment, write an input YAML for <protein sequences and ligands> following docs/prediction.md, and run `boltz predict input_path --use_msa_server`. Tell me where the predicted structures were written.

Caveat. Predictions are model outputs, not experimental structures; validate anything you act on.

Use this in your AI agent

Ask your agent

Using the Deduped MCP, get the setup steps for jwohlwend/boltz and "Predict a protein complex structure with Boltz"

Add Deduped to Claude Code once

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

Cursor, ChatGPT, others

Share: X LinkedIn Hacker News Email Copy link

Third-party repos we don't own. AI-written use cases can be wrong. Disclaimer