{
 "schema_version": 1,
 "generated": "2026-10-31",
 "id": "jwohlwend-boltz--screen-ligands-for-binders-with-boltz-affinity",
 "repo": "jwohlwend/boltz",
 "repo_url": "https://github.com/jwohlwend/boltz",
 "repo_slug": "jwohlwend-boltz",
 "title": "Screen small molecules for likely binders",
 "page_title": "How to screen small molecules for likely binders with Boltz",
 "summary": "Use Boltz-2's affinity output to separate likely binders from decoys in a hit-discovery screen.",
 "who": "A drug discovery scientist triaging a list of candidate ligands against one target.",
 "problem": "Physics-based free-energy methods are accurate but far too slow to run on every candidate in a screen.",
 "outcome": "A per-ligand affinity_probability_binary score from 0 to 1 that ranks which molecules look like binders.",
 "steps": [
  "Install with `pip install boltz[cuda] -U`",
  "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",
  "Read affinity_probability_binary for each ligand to detect binders from decoys",
  "Send only the top candidates on to slower methods or the lab"
 ],
 "agent_prompt": "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.",
 "agents": [
  "claude-code",
  "codex",
  "cursor",
  "gemini-cli"
 ],
 "difficulty": "Advanced",
 "time": "half a day",
 "basis": "readme",
 "caveat": "The README says affinity_probability_binary is for hit discovery and affinity_pred_value for lead optimization; do not mix them up.",
 "category": "Security and science",
 "tags": [
  "Security and science"
 ],
 "lang": "python",
 "requirements": [
  "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)"
 ],
 "risk": "none",
 "seen_in_the_wild": false,
 "mentioned_publicly": false,
 "risks": [],
 "best": false,
 "score": 0.9,
 "evidence": [],
 "url": "https://dedupedai.com/use-cases/jwohlwend-boltz/screen-ligands-for-binders-with-boltz-affinity/",
 "md": "https://dedupedai.com/use-cases/jwohlwend-boltz/screen-ligands-for-binders-with-boltz-affinity/index.md",
 "disclaimer": "Deduped lists open-source repositories that belong to other people. We do not own, maintain, audit, or vouch for any of them, and a repo appearing here is not an endorsement or a safety check. The use cases, steps, and prompts are written by AI and may be incomplete, outdated, or just wrong. Where a use case is marked \"Seen in the wild\", we link to public posts where someone described something similar, but we have not verified those posts and the use case itself is still our AI's own write-up. Use all of this at your own risk. Only run code, commands, or agents on systems and accounts you are authorized to use, and read the code and every command before you run it, especially anything that touches credentials, files, or the network. Nothing here is professional, security, legal, or financial advice. All trademarks and project names belong to their respective owners, and their use here does not imply affiliation. Content is provided as is, without warranties of any kind. Found a mistake, a safety problem, or something you want removed? Email hello@dedupedai.com and we will look at it promptly.",
 "api": "https://dedupedai.com/api/v1/usecases/jwohlwend-boltz--screen-ligands-for-binders-with-boltz-affinity.json",
 "api_version": "v1"
}