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How to pick the right AlphaFold 3 weights for your project with Alphafold3

Compare the standard weights with the SynthID Bio-structure and Leaving Atom variants before you run.

Short answer: Read the Obtaining Model Parameters section and the linked WEIGHTS_TERMS_OF_USE.md; then Note the SynthID Bio-structure version, which predicts watermarked structures, and the AF3 Leaving Atom variant fine-tuned for leaving atom handling; For non-commercial one-off work consider alphafoldserver.com, which the README says has a more limited set of ligands and covalent modifications. All steps.

Credentials. All weight variants are subject to the AlphaFold 3 weights terms of use.

Who it is forA team deciding how to run AlphaFold 3 for commercial or watermarked work.

The problemPicking the wrong weights or the wrong route can break the terms you agreed to.

The outcomeA clear decision on which weights and which route fit your use.

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. Read the Obtaining Model Parameters section and the linked WEIGHTS_TERMS_OF_USE.md
  2. Note the SynthID Bio-structure version, which predicts watermarked structures, and the AF3 Leaving Atom variant fine-tuned for leaving atom handling
  3. For non-commercial one-off work consider alphafoldserver.com, which the README says has a more limited set of ligands and covalent modifications
  4. For commercial use follow the README pointer to Gemini Enterprise Agent Platform on Google Cloud

Prompt for your agent

Using google-deepmind/alphafold3, compare the standard, SynthID Bio-structure and Leaving Atom weights plus the server and Google Cloud routes for <my project>, and tell me which fits.

Caveat. This is a reading and decision task; it does not run a prediction.

Use this in your AI agent

Ask your agent

Using the Deduped MCP, get the setup steps for google-deepmind/alphafold3 and "Pick the right AlphaFold 3 weights for your project"

Add Deduped to Claude Code once

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

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