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

How to screen small molecules for likely binders with Boltz

Use Boltz-2's affinity output to separate likely binders from decoys in a hit-discovery screen.

Short answer: Install with pip install boltz[cuda] -U; then write one YAML per protein and ligand pair that asks for the affinity property, as described in docs/prediction.md; put the YAML files in one directory and run boltz predict input_path --use_msa_server on that directory for batched processing. All steps.

Who it is forA drug discovery scientist triaging a list of candidate ligands against one target.

The problemPhysics-based free-energy methods are accurate but far too slow to run on every candidate in a screen.

The outcomeA per-ligand affinity_probability_binary score from 0 to 1 that ranks which molecules look like binders.

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. Install with pip install boltz[cuda] -U
  2. Write one YAML per protein and ligand pair that asks for the affinity property, as described in docs/prediction.md
  3. Put the YAML files in one directory and run boltz predict input_path --use_msa_server on that directory for batched processing
  4. Read affinity_probability_binary for each ligand to detect binders from decoys
  5. Send only the top candidates on to slower methods or the lab

Prompt for your agent

With jwohlwend/boltz, build a directory of YAML inputs pairing <target protein> with each ligand in <list>, requesting affinity, and run `boltz predict input_path --use_msa_server` on it. Rank the ligands by affinity_probability_binary.

Caveat. The README says affinity_probability_binary is for hit discovery and affinity_pred_value for lead optimization; do not mix them up.

Use this in your AI agent

Ask your agent

Using the Deduped MCP, get the setup steps for jwohlwend/boltz and "Screen small molecules for likely binders"

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