NVIDIA-BioNeMo/bionemo-agent-toolkit

NVIDIA-BioNeMo/bionemo-agent-toolkit

Skill Claude Code

End-to-end Proteina-Complexa design pipeline driver. Use when the user wants to "design a binder", "design binders for X", "run complexa design", "de novo binder", "PDL1 binder", "TrkA binder", "design proteins for target", "protein binder design", "ligand binder", "design a small-molecule binder", "ATP-binding…

NVIDIA-BioNeMo/bionemo-agent-toolkit

Skill Claude Code

Standalone evaluation of an existing PDB directory with Proteina-Complexa. Use when the user wants to "evaluate PDB files", "re-fold these designs", "compute interface pAE", "compute ipLDDT for a folder", "run AF2 / RF3 / ESMFold on my designs", "score binder candidates", "designability of this folder", "scRMSD for…

NVIDIA-BioNeMo/bionemo-agent-toolkit

Skill Claude Code

First-time setup, environment configuration, and model-weight installation for Proteina-Complexa. Reach for this skill whenever the user says "set up complexa", "install complexa", "configure my environment file", "first-time setup", "what models do I have installed", "what's in my environment file", "download model…

NVIDIA-BioNeMo/bionemo-agent-toolkit

Skill Claude Code

Use this skill whenever the user wants to run a parameter sweep over a Proteina-Complexa design pipeline — cartesian-product hyperparameter scans, Pareto search over generation/reward/evaluation knobs, or any "compare configurations" workflow. Trigger phrases include "sweep beam width", "sweep nsteps", "hyperparameter…

NVIDIA-BioNeMo/bionemo-agent-toolkit

Skill Claude Code

Use this skill whenever the user wants to add, register, edit, list, show, or validate a Proteina-Complexa design target for any pipeline — protein binder (default), ligand binder, or AME / enzyme scaffolding. Triggers include "add a target", "define a new target for binder design", "register a hotspot", "set up a…