Battle-tested-Research-Prompts/prompts/anthropic-protein-binder-design

De Novo Protein Binder Design Campaign

Lab	Anthropic
Model	Claude Mythos Preview and Opus 4.8 (Claude Science agent harness)
Field	Computational biology — de novo miniprotein binder design
Result (yield)	Wet-lab-validated binders against 14 of 15 targets (354 binders from 1,320 designs). Hit rates 22.6–35.1% vs. the 10–15% typical of human campaigns; high-affinity binders (KD < 10 nM) against ≥6 targets; best designs exceeded published state-of-the-art affinities (e.g. RBX1: 40% hit rate vs. 3.7% for competition winners). Validated independently by Adaptyv Bio and Twist Bioscience.
Date	August 18, 2026
Announcement	https://www.anthropic.com/research/Claude-accelerates-protein-design
Prompt release (CC-BY-4.0)	https://huggingface.co/datasets/Anthropic/claude-protein-binder-design

Why it's battle-tested

A ~30,000-token campaign prompt ran autonomously for 48 hours (multi-target mode, up to 12,500 H100-hours) or 24 hours per target (single-target mode), with no scientific guidance from humans — producing experimentally confirmed binders that match or beat expert human designs.

Prompt architecture

• multi-target-prompt.md — the full 14-target campaign prompt (~114 KB), carried as system context by every agent at every depth. Specifies task, all 14 targets with UniProt IDs and oligomeric states, a curated reference corpus, design/folding tools, budgets, spend ceilings, safety gates, scoring, and deliverables.
• multi-target-kickoff.md — the user message that starts the campaign: a single, precise instruction block with an ordered first-actions list, clock definition (T0 + 48 h), and "Do not ask me any questions or wait for approval."
• single-target-kickoff.md — the 24-hour, $10k single-target variant.

Notable techniques: explicit sub-agent scope discipline ("your authoritative SCOPE is your task brief from your parent"), spend governors with hard ceilings, originality/novelty checks, counter-target selectivity requirements (GDF-8 vs. GDF-11), and verified-figure grounding.

Hidden user prompts (unpublished)

Per the HF release, the campaign prompts assume the Claude Science agent harness (host.delegate, host.compute, submit_gate, wait_for_notification, Modal sandboxes, Slack, Drive) — "a public reader reproducing the campaign must supply equivalents." Unpublished user-authored context:

• The Claude Science harness system prompt and tool/skill definitions.
• Any project instructions (CLAUDE.md-equivalents) in the campaign workspace.
• The pre-approved network domains and connector configuration left by the setup session.

The campaign and kickoff prompts above are, however, the complete published instruction set — the substantive campaign specification is fully in hand.

Excluded from this entry

The companion analytical-chemistry prompts (two-sentence NMR / LC-MS messages from the same announcement) were removed: their yield is attributable almost entirely to the unpublished Claude Science harness and skills, not to the published one-liners. Same character as the deleted Riemann-zeta entry (see root README).

Files

Runnable prompts (verbatim, copy-paste):

• multi-target-prompt.md — the 14-target campaign prompt, loaded as system context (verbatim from the HF release).
• multi-target-kickoff.md — first user message, multi-target campaign.
• single-target-kickoff.md — first user message, single-target campaign.

Further reading

• Technical report: https://www-cdn.anthropic.com/30bf50e22a01388bb29bf077ee3f244531594b7a.pdf
• Chemical analysis technical report: https://www-cdn.anthropic.com/9f08da5189ac269b3242ca760de9823805c3f5f6.pdf
• Single-target prompts (16 targets incl. GDF-8-latent): see prompts/single_target/ in the HF dataset.