complexa-evaluate-pdbs SKILL.md skillA
complexa-evaluate-pdbs from nvidia/skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add nvidia/skills/complexa-evaluate-pdbs@git:20261021.69abc15Pins git:20261021.69abc15 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- nvidia/skills
- Path
skills/bionemo-complexa-evaluate-pdbs/SKILL.md- Versions recorded
- 1
- Latest version
- git:20261021.69abc15, committed Oct 21, 2026
- Size
- 13,042 bytes
- Repository stars
- 3,871
- License
- Apache-2.0
Agent runbook for evaluating an existing PDB directory through the separately installed first-party Proteina-Complexa CLI. Use to refold or score designs, compute interface pAE, i_pLDDT, scRMSD, motif RMSD, or designability, run complexa analysis, or assess third-party BindCraft, AlphaProteo, or RFdiffusion outputs. SKILL.md selects and invokes the evaluation configuration; bundled executables only inspect local readiness and write a run manifest.
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/skills/complexa-evaluate-pdbs@sha256:0fbdb6f6dfe5411cThe line at the top of this page pins the label git:20261021.69abc15, 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_obeiogqvl3neiyet)
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Versions
The registry has recorded 1 version of this file, committed on Oct 21, 2026.
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 (13042 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/skills · 3,871 stars · license Apache-2.0 · pushed 2026-11-05 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_obeiogqvl3neiyet GET https://markdownregistry.com/api/v1/resolve?ref=nvidia/skills/complexa-evaluate-pdbs GET https://markdownregistry.com/api/v1/blob/0fbdb6f6dfe5411cc8c6eb70a5e6a7a6a55ddc3569c89ed7ef2806c6d5bcd014
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.