{
 "schema_version": 1,
 "generated": "2026-10-31",
 "id": "jwohlwend-boltz--compare-ligand-modifications-with-boltz",
 "repo": "jwohlwend/boltz",
 "repo_url": "https://github.com/jwohlwend/boltz",
 "repo_slug": "jwohlwend-boltz",
 "title": "Compare small changes to a lead molecule",
 "page_title": "How to compare small changes to a lead molecule with Boltz",
 "summary": "Use affinity_pred_value to see how small modifications change predicted binding during hit-to-lead work.",
 "who": "A medicinal chemist choosing which analogs of a lead compound to synthesise next.",
 "problem": "Synthesising and assaying every analog is slow and expensive.",
 "outcome": "Predicted log10(IC50) values for each analog, so you can prioritise which ones to make.",
 "steps": [
  "Install from GitHub for daily updates if you want the newest code: `git clone https://github.com/jwohlwend/boltz.git` then `cd boltz; pip install -e .[cuda]`",
  "Write YAML inputs for the lead and each modified analog against the same target, requesting affinity",
  "Run `boltz predict input_path --use_msa_server` on the directory of inputs",
  "Compare affinity_pred_value, reported as log10(IC50) derived from an IC50 in micromolar, across analogs",
  "Use the results to rank which analogs to synthesise first"
 ],
 "agent_prompt": "Using jwohlwend/boltz, predict affinity for my lead compound <SMILES> and these analogs <list> against <target>, then make a table of affinity_pred_value per analog with a note on which modifications helped.",
 "agents": [
  "claude-code",
  "codex",
  "cursor",
  "gemini-cli"
 ],
 "difficulty": "Advanced",
 "time": "half a day",
 "basis": "readme",
 "caveat": "Updated Boltz-2 evaluation and training code are marked as coming soon in the README.",
 "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": 0.8,
 "evidence": [],
 "url": "https://dedupedai.com/use-cases/jwohlwend-boltz/compare-ligand-modifications-with-boltz/",
 "md": "https://dedupedai.com/use-cases/jwohlwend-boltz/compare-ligand-modifications-with-boltz/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--compare-ligand-modifications-with-boltz.json",
 "api_version": "v1"
}