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…
NVIDIA-BioNeMo/bionemo-agent-toolkit
Plugin Claude Code
Bundles 2 skills · 276 tokens together
NVIDIA BioNeMo agent skills for life sciences — protein folding, molecular docking, generative chemistry, genomics, protein design, and biomarker discovery as ready-to-call tools.
NVIDIA-BioNeMo/bionemo-agent-toolkit
Cursor rule Cursor
Side-by-side comparison of the two de novo binder-design routes (complexa-binder-design vs protein-binder-design) to help choose one for a given target and constraints.
NVIDIA-BioNeMo/bionemo-agent-toolkit
Cursor rule Cursor
Route selection and orchestration for de novo protein binder design. Composes two independent binder-design skills — complexa-binder-design (Proteina-Complexa reward-guided co-design) and protein-binder-design (RFdiffusion + ProteinMPNN + Boltz2/OpenFold3 NIM orchestration). Each resolves a target and hotspots…
NVIDIA-BioNeMo/bionemo-agent-toolkit
Skill Codex
Validate coding-sequence CSVs, extract public CodonFM/Encodon embeddings, and choose checkpoints for downstream property modeling.
NVIDIA-BioNeMo/bionemo-agent-toolkit
Skill Codex
Fine-tune public CodonFM Encodon checkpoints on labeled coding-sequence or coding-variant data using LoRA, head-only, or full fine-tuning. Use when a user explicitly asks to fine-tune CodonFM or Encodon for regression or classification. Support generic public-v1 Encodon workflows only; reject Decodon, MissenseDataset…
NVIDIA-BioNeMo/bionemo-agent-toolkit
Skill Codex
Validate, prepare, or run public CodonFM Encodon masked-codon variant scoring and review compatibility of its scoring workflows. Use only when the user explicitly requests CodonFM or Encodon, or that context is already established in the conversation. Do not select this skill for a generic variant-scoring request…
NVIDIA-BioNeMo/bionemo-agent-toolkit
Skill Codex
Set up the public CodonFM v1 repository and download public Encodon checkpoints. Use for requests to build or launch the CodonFM development container, configure local data/checkpoint mounts, verify GPU access, or download public Encodon 80M, 600M, 1B, or Cdwt-1B weights. Do not use for Decodon, Encodon 5B/10B…
Skill Claude CodeCodex
Use when writing or debugging nvMolKit Python code for GPU-accelerated RDKit fingerprints, similarity, conformers, clustering, and molecular searches.
Plugin Claude Code
Bundles 10 skills, 2 hooks · 1,471 tokens together
Integrate DTensor-based context parallelism (CP) into a custom co-folding / structure-prediction model — sharding the O(N²) pair and attention tensors across a multi-GPU device mesh via explicit ring/transpose collectives. A top-level cpizemodelworkflow conductor prioritizes, sequences, and gates the whole effort end.
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