Msa Structure Prediction Pipeline — Agent Skill by NVIDIA

From the author

NOTE: your protein sequence and the retrieved MSA alignment are transmitted to external NVIDIA-hosted APIs (health.api.nvidia.com) on every call. Use local NIM containers for confidential or proprietary sequences. Run a complete protein structure prediction pipeline using NVIDIA BioNeMo NIMs: search for MSA alignments with MSA-Search (ColabFold), then predict the structure with OpenFold3 using the retrieved alignments. Use this skill whenever the user wants to predict a protein structure with maximum accuracy using MSA context, run the full AlphaFold3-style pipeline, generate MSA-informed structure predictions, or improve structure prediction accuracy by providing evolutionary information. Triggers on: MSA structure prediction pipeline, structure prediction pipeline, MSA-informed prediction, OpenFold3, ColabFold MSA, AlphaFold3 pipeline, protein structure, homology search, a3m alignment, UniRef30, NIM microservice. This pipeline chains MSA-Search and OpenFold3.

— the description by NVIDIA

Install

Get the skill from its source (we cannot redistribute it):
https://github.com/NVIDIA/skills/tree/fce3cca4170be75e82c64920654d56ee2811b005/skills/bionemo-msa-structure-prediction-pipeline

Documentation by NVIDIA

The licence of this skill does not allow us to copy its documentation. Read it at the source

Files

BENCHMARK.md(opens on GitHub)Not mirrored: opens on GitHub7.7 KiB
SKILL.md(opens on GitHub)Not mirrored: opens on GitHub6.4 KiB
evals/evals.json(opens on GitHub)Not mirrored: opens on GitHub7.8 KiB
skill-card.md(opens on GitHub)Not mirrored: opens on GitHub4.1 KiB
skill.oms.sig(opens on GitHub)Not mirrored: opens on GitHub4.5 KiB

Requirements and compatibility

Works with: Claude Code, Claude apps, OpenAI Codex, GitHub Copilot, Cursor, Gemini CLI, Kiro, OpenCode, Goose, Amp, Roo Code, JetBrains Junie, Factory Droid, Devin (ex-Windsurf), Mistral Vibe, OpenHands, Letta

“Works with” means the tool reads the open Agent Skills format; a skill written for one tool may use features others lack.

Needs: Declares allowed tools, Needs an API key, Needs Python

Security

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