complexa-evaluate-pdbs SKILL.md skillA
This file is byte-identical to the first copy the registry indexed. Same content hash, so the same checks give both the same grade.
complexa-evaluate-pdbs from nvidia-bionemo/bionemo-agent-toolkit is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add nvidia-bionemo/bionemo-agent-toolkit/complexa-evaluate-pdbs@git:20261016.a6eced5Pins git:20261016.a6eced5 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- nvidia-bionemo/bionemo-agent-toolkit
- Path
skills/bionemo-agent-toolkit/skills/complexa-evaluate-pdbs/SKILL.md- Versions recorded
- 2
- Latest version
- git:20261016.a6eced5, committed Oct 16, 2026
- First version recorded
- Aug 25, 2026
- Size
- 13,544 bytes
- Repository stars
- 503
- License
- a license file GitHub does not identify
Standalone evaluation of an existing PDB directory with Proteina-Complexa. Use this skill whenever the user wants to "evaluate PDB files", "re-fold these designs", "compute interface pAE", "compute i_pLDDT for a folder", "run AF2 / RF3 / ESMFold on my designs", "score binder candidates", "designability of this folder", "scRMSD for designs", "motif RMSD for these PDBs", "complexa analysis", "complexa evaluate from a PDB directory", "evaluate from pdb dir", or score third-party outputs…
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# Complexa Evaluate-PDBs Skill Score a directory of pre-existing PDB files against the same metrics Proteina-Complexa uses internally. Wraps `complexa analysis <evaluate_config> ++sample_storage_path=<dir>`: the CLI runs the `evaluate` step (refold + interface metrics + monomer metrics) and then the `analyze` step (success thresholds, diversity, pass-rate CSVs). Do **not** run `complexa generate` here — the inputs already exist. ## What this skill enables - Re-fold a directory of designed PDBs with AF2 (`colabdesign`), RF3 (`rf3_latest`), ESMFold (`esmfold`), or Boltz2 (`boltz2_default`). - Compute binder interface metrics: `i_pAE`, `min_ipAE`, `i_pTM`, `pLDDT`, binder/complex scRMSD. - Compute monomer **designability** (ProteinMPNN-redesigned scRMSD) and **codesignability** (original sequence refold scRMSD). - For motif inputs: motif RMSD (CA + all-atom), motif-region designability/codesignability, sequence recovery. - Aggregate into per-PDB CSVs plus pass-rate summaries using the default thresholds for the `result_type`. ## Step 1: Pre-flight Always check GPU / disk / tool binaries before launching a refold job. RF3 and ColabDesign-AF2 are large. ```bash …
Read the whole file at its exact version.
How to install
mdr add nvidia-bionemo/bionemo-agent-toolkit/complexa-evaluate-pdbs@sha256:06ef38789516c2b9The line at the top of this page pins the label git:20261016.a6eced5, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_yzjcrfxnt57djlzu)
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Versions
The registry has recorded 2 versions of this file, between Aug 25, 2026 and Oct 16, 2026, about one every 52 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20261016.a6eced5 latest | 2026-10-16 | a6eced5 | 13,544 B | A | view · diff |
| git:20260825.0e67a61 | 2026-08-25 | 0e67a61 | 13,394 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (13544 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
nvidia-bionemo/bionemo-agent-toolkit · 503 stars · license a license file GitHub does not identify · pushed 2026-11-05 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_yzjcrfxnt57djlzu GET https://markdownregistry.com/api/v1/resolve?ref=nvidia-bionemo/bionemo-agent-toolkit/complexa-evaluate-pdbs GET https://markdownregistry.com/api/v1/blob/06ef38789516c2b9f2a25dcc6321d016ae8d08f4a6c4d8cc796e64e89a2c0b6f
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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