binder-design-campaign

Protein design campaign

Three branches, one core. First turn the user's goal into a reviewable campaign plan; after the user chooses how far to execute, the evidence rules and deliverable discipline below hold for all three branches.

Provenance and rationale: docs/ and NOTICE.md, relative to this skill.

Non-negotiables

These hold at every depth, including inside sub-agents, and bind hardest on the steps nobody is watching.

1. State only what you established. Every claim in a report, update or manifest traces to an executed computation or a saved artifact you can point at. Verified means you ran the check and hold its output.
2. Every external identifier is fetched. DOIs, PMIDs, PDB IDs, UniProt accessions, residue ranges and URLs in any deliverable are the literal output of a lookup executed in this session.
3. Anomalies are bugs until investigated. A score of exactly zero, a gate that passes everything, a gate that fails everything, a constant metric, a perfect metric, an impossible runtime, zero variance across seeds: halt that stage, diagnose, then proceed.
4. Cheapest falsifying check first. Run the seconds-scale check that could kill a plan before committing hours of GPU to it.
5. Lead with the unfavourable reading. Headline the worst defensible interpretation of your own data. Disclose deviations from the stated method, and name analyses tuned after seeing results along with how many configurations you tried. Report inconclusive results as inconclusive.
6. The instrument is a filter, never an oracle. In silico confidence ranks designs within a target. It does not tell you whether a target will work, and it relates only weakly to affinity — measured, not assumed (references/failure-modes.md §1). Every summary you write says so.
7. Verify inherited inputs. Check target structures, construct definitions and hotspot numbering against their primary source before building on them.
8. Scope. This protocol is in silico and it ends at the design sheet. Validation is in vitro, by the user or a CRO; analysing returned assay data is a different task and does not run under these gates. Results from an earlier round enter here as operator input at G0, never as something this protocol goes and fetches. Work on select agents or toxins, and enhancement of pathogen function, is out of scope: stop and say so. See docs/responsible-use.md.