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Sign protein-binder-design & Complexa-binder-design - #50

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ohadmo wants to merge 13 commits into
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omosafi/protein-binder-design-workflow

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@ohadmo ohadmo commented Oct 1, 2026

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ohadmo commented Oct 1, 2026

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@greptileai

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ohadmo commented Oct 1, 2026

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/nvskills-ci

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greptile-apps Bot commented Oct 1, 2026 •

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RetriggerConfidence Score: 4/5

[Medium impact] Renames workflow directory and updates skill documentation.

The PR does not appear safe to merge until the distributed skills’ signatures match their current guidance.

Findings

  1. P1 Signatures do not match skills ▶

Summary

The PR packages and signs two protein-binder-design skills, updates their guidance and supporting workflows, and moves workflow sources to workflow-skills/. Since the previous review, it changes three Complexa Skillspector exceptions from fingerprint-based suppressions to file-and-message rules.

Reviews (12) · Last reviewed commit: "fix credential exceptions across LLM sca..." · Reviewed by Greptile

Comment thread workflows/generative-protein-binder-design/protein-binder-design/evals/README.md Outdated
ohadmo added 4 commits October 1, 2026 16:39
Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>
Add an explicit Boltz2 composite-confidence filter and ranked CSV export, normalize hosted NIM credentials for delegated commands, and defer live campaign evaluations until verified fixtures exist. Add a staged offline bookkeeping evaluation with regression coverage.

Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>
Move the native workflow sources out of the NVCarps workflows prefix so generated skills are validated individually. Update plugin discovery, catalog paths, CI filters, and documentation for the new source root.

Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>
Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>
@ohadmo
ohadmo force-pushed the omosafi/protein-binder-design-workflow branch from ec35243 to 1213167 Compare October 1, 2026 23:39
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ohadmo commented Oct 1, 2026

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ohadmo commented Oct 1, 2026

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Signed-off-by: nvskills-svc-account <svc-nvskills-signing@nvidia.com>
Comment thread skills/bionemo-agent-toolkit/skills/complexa-binder-design/skill-card.md Outdated
ohadmo added 2 commits October 1, 2026 17:46
Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>
Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>
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ohadmo commented Oct 2, 2026

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Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>
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… evals

Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>
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ohadmo commented Oct 2, 2026

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@ohadmo ohadmo changed the title Sign protein-binder-design Sign protein-binder-design & Complexa-binder-design Oct 2, 2026
Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>
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ohadmo force-pushed the omosafi/protein-binder-design-workflow branch from daf9359 to 4ee2449 Compare October 2, 2026 22:55
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Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>
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ohadmo commented Oct 8, 2026

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Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>
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ohadmo commented Oct 8, 2026

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description: >
Run a complete protein binder design campaign with NVIDIA Proteina-Complexa: resolve a target structure and hotspots from a name/sequence/PDB, co-design binder sequence+structure with reward-guided test-time search (best-of-n, beam search, FK steering, MCTS), select with the internal AF2 reward gate, then INDEPENDENTLY validate each binder by refolding the complex with Boltz2 (default) or OpenFold3 and rank on interface confidence, pLDDT, ipSAE, apo/holo stability, and hotspot contact. Use whenever the user wants de novo binders against a named target, sequence, or PDB, hotspot/epitope-targeted design, Proteina-Complexa / Complexa, or ranked validated binders from one request. Sibling of protein-binder-design (RFdiffusion + ProteinMPNN); this skill uses Proteina-Complexa.
description: Design protein binders with Proteina-Complexa and independently validate them with Boltz2. Use for design campaigns, not code or report review.
metadata:

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P1 Signatures do not match skills

This skill’s guidance changed after its signature was produced. The signature records a different SKILL.md hash, so consumers cannot verify the guidance being packaged. The protein-binder-design skill has the same mismatch. Regenerate both signatures for the final payload.

Knowledge Base Used: Skill quality and compliance controls

Signed-off-by: Ohad Mosafi <omosafi@nvidia.com>
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ohadmo commented Oct 9, 2026

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