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

How to predict a biomolecular complex from a JSON input with Alphafold3

Write a fold_input.json for your sequences and run the container to get a predicted structure.

Short answer: Follow the installation documentation in docs/installation.md and obtain the model parameters from Google; then write a fold_input.json with name, sequences, modelSeeds, dialect Alphafold3 and version 1, as in the README example. All steps.

Credentials. Model parameters may only be used if received directly from Google and are subject to their terms of use.

Who it is forA structural biologist who needs a prediction for a specific complex.

The problemPublic servers limit ligands, modifications and throughput.

The outcomeA predicted structure written to your output directory.

What you need first

  • The model parameters, which you may only use if received directly from Google, under the weights terms of use
  • Docker and an NVIDIA GPU for the inference step
  • The genetic and template databases for the data pipeline, mounted into the container
  • A fold_input.json describing your sequences, model seeds, dialect and version

Steps

  1. Follow the installation documentation in docs/installation.md and obtain the model parameters from Google
  2. Write a fold_input.json with name, sequences, modelSeeds, dialect Alphafold3 and version 1, as in the README example
  3. Run the docker command in the README with volumes for af_input, af_output, the model parameters and the public databases, calling python run_alphafold.py with --json_path, --model_dir and --output_dir
  4. Read docs/output.md to interpret the files you get back

Prompt for your agent

Using google-deepmind/alphafold3, write a fold_input.json for <my sequences>, run the documented docker command with my model and database directories, and explain the output files.

Caveat. The repo contains the inference pipeline only; it does not include the model parameters.

Use this in your AI agent

Ask your agent

Using the Deduped MCP, get the setup steps for google-deepmind/alphafold3 and "Predict a biomolecular complex from a JSON input"

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