What is boltz-protein-screen?

A tool for testing an existing library of protein sequences—such as peptides, antibodies, nanobodies, or other binders—against a target and ranking the results.

Use it to screen known protein candidates against a target, rank likely binders, and download predicted structures for individual hits.

It removes the need to evaluate each supplied candidate separately. It accepts libraries from sequence text, FASTA, CSV, or similar files and returns binding and structure measurements.

boltz-protein-screen — Skill for Codex by boltz-bio/boltz-api-skills

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent

npx skills add boltz-bio/boltz-api-skills --skill boltz-protein-screen

Clone the repo

git clone --depth 1 https://github.com/boltz-bio/boltz-api-skills

Made for: Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/skills/boltz-bio/boltz-api-skills/boltz-protein-screen/github.svg)](https://agentmods.dev/skills/boltz-bio/boltz-api-skills/boltz-protein-screen)

Your own site

<a href="https://agentmods.dev/skills/boltz-bio/boltz-api-skills/boltz-protein-screen"><img src="https://agentmods.dev/badge/skills/boltz-bio/boltz-api-skills/boltz-protein-screen/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/skills/boltz-bio/boltz-api-skills/boltz-protein-screen"><img src="https://agentmods.dev/badge/skills/boltz-bio/boltz-api-skills/boltz-protein-screen.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 46 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 1,829 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.00046	$0.01829
Opus 5.5	$0.00018	$0.00732
Sonnet 5.5	$0.00009	$0.00366
Haiku 4.5	$0.00005	$0.00183

Measured 2mo ago against content hash 101149e875f8, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

boltz-protein-screen scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2mo ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

plugins/boltz-api-cli/skills/boltz-protein-screen/SKILL.md · 76 lines

How it starts

The opening of the file, as written. The whole thing — 76 lines — stays where its author put it; the contents beside it link to each section on GitHub.

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 proteins / peptides / antibodies / nanobodies.

Normalize the binder library into proteins — a list of candidate complexes. For a simple sequence library each entry has one protein entity; multi-chain candidates (antibody heavy+light) are also allowed.
Pick the target variant:
- structure_template — user has a CIF/PDB file or URL; select which chains are polymer vs ligand, which residues to keep (crop_residues), and optionally epitope_residues / flexible_residues.
- no_template — user has only sequences; pass them as target.entities plus optional epitope_residues.
Don't add bonds / constraints unless the user asks for geometry constraints.
Author the payload YAML or JSON, run estimate-cost, show the USD cost, wait for explicit confirmation.
start to submit. Capture the ID.
Launch download-results through the runtime's long-running or non-blocking command facility. Use the mechanism the runtime documents; consult boltz-cli-setup if unsure. After launching the downloader, always report the job ID, run name, and output directory. If the runtime can schedule follow-up checks, schedule a download-status check and state the cadence; otherwise include the download-status command.
Rank hits from <output-root>/<run-name>/results/index.jsonl by binding_confidence descending. Use iptm and min_interaction_pae as tiebreakers. optimization_score is not emitted for this endpoint. Read references/results.md for output layout and metric details.

Read the full file on GitHub · 76 lines

Files

What ships with it

3 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

2mo ago Changed · +8 lines · -32 tokens per session 101149e875f8
2mo ago First seen · 68 lines · 78 tokens per session scan A ad14828377be

Subscribe to this mod's changes

boltz-protein-screen is a skill published in the GitHub repository boltz-bio/boltz-api-skills (5 stars, last pushed 13d ago), licensed MIT. It adds 46 tokens to every session and 1,829 once invoked, about $0.0002 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

Scientific

boltz-protein-screen next to 6 skills from other repositories
Mod	Type	Stars	Last push	Licence	Scan	Tokens	Works with
boltz-protein-screenboltz-bio/boltz-api-skills	Skill	5	13d ago	MIT	A	46	Codex
instrument-data-to-allotropeanthropics/knowledge-work-plugins	Skill	35k	2d ago	Apache-2.0	A	123	Claude Code
exploratory-data-analysisK-Dense-AI/scientific-agent-skills	Skill	56k	4d ago	MIT	A	83	Claude Code
matlabK-Dense-AI/scientific-agent-skills	Skill	56k	4d ago	MIT	A	44	Claude Code
phylogeneticsK-Dense-AI/scientific-agent-skills	Skill	56k	4d ago	MIT	A	71	Claude Code, Codex
research-engineerdavila7/claude-code-templates	Skill	33k	yesterday	MIT	A	43	Claude Code, Codex
mapping-to-snomedmaziyarpanahi/openmed	Skill	5.8k	yesterday	Apache-2.0	A	205	Claude Code