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boltz-small-molecule-screen

Skill

Screen existing small-molecule libraries with Boltz. Use when docking, scoring, or ranking a supplied SMILES or compound library against a target; also returns free Tier-1 ADME/ADMET (solubility, permeability, lipophilicity/logD) per molecule. Not for de novo molecule design, one-off docking, or ADM

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Install

git clone https://github.com/boltz-bio/boltz-api-skills.git ~/.claude/skills/boltz-small-molecule-screen

What is boltz-small-molecule-screen?

Screen existing small-molecule libraries with Boltz. Use when docking, scoring, or ranking a supplied SMILES or compound library against a target; also returns free Tier-1 ADME/ADMET (solubility, permeability, lipophilicity/logD) per molecule. Not for de novo molecule design, one-off docking, or ADME on bare SMILES with no target (use boltz-small-molecule-adme).

What this can do

Capabilities declared in this component's own frontmatter — not inferred.

Inherit all session tools

Declares no tool restrictions — inherits every session tool

~91 tokens of context used while enabled, before you invoke anything

Documentation

README · ~5 min read

Workflow

If boltz-api is missing from PATH, use boltz-cli-setup for install/update guidance before retrying. If a command reports missing or expired authentication, use boltz-cli-setup to start boltz-api auth login --device-code before retrying; do not ask permission first. If the agent host sandbox blocks boltz-api install/auth/API calls, use boltz-cli-setup to request the host sandbox bypass/escalation needed for user-wide CLI install, browser login, credential storage, temp files, or API access before retrying.

Use this skill when the user already has candidate molecules.

  1. Normalize the library from raw SMILES, a CSV (auto-detect the SMILES column), .smi, or .txt into the molecules list. Each entry is {smiles, id?}; the optional id is echoed back as external_id on each result.
  2. Normalize the target: one or more protein sequences into target.entities, plus optional pocket_residues (0-based) and/or reference_ligands (SMILES of known binders to help locate the pocket).
  3. Keep default server-side filtering unless the user asks for custom filters — only add molecule_filters on explicit request.
  4. Author the payload YAML or JSON, run estimate-cost, show the USD cost, wait for explicit confirmation.
  5. start to submit (synchronous). Capture the ID.

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