nvidia-bionemo/bionemo-agent-toolkit

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boltz2-nim Use Boltz2 NIM for biomolecular structure prediction and binding affinity. Invoke for Boltz2, protein structures, pro…

nvidia-bionemo/bionemo-agent-toolkit

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diffdock-nim Run DiffDock molecular docking via NVIDIA NIM to predict small-molecule binding poses against protein targets. Use fo…

nvidia-bionemo/bionemo-agent-toolkit

225

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drug-discovery-pipeline NOTE: molecule and target inputs and your NGC_API_KEY are transmitted to external NVIDIA-hosted API endpoints on ever…

nvidia-bionemo/bionemo-agent-toolkit

223

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genmol-nim Generate novel drug-like molecules using the GenMol NIM microservice. Use for de novo generation, scaffold decoration…

nvidia-bionemo/bionemo-agent-toolkit

217

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openfold3-nim Use this skill for OpenFold3, NVIDIA's BioNeMo NIM microservice for biomolecular structure prediction. Invoke wheneve…

nvidia-bionemo/bionemo-agent-toolkit

209

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msa-search-nim Generate multiple sequence alignments (MSAs) for protein sequences using the ColabFold MSA-Search NIM. Use for homolo…

nvidia-bionemo/bionemo-agent-toolkit

207

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molmim-nim Use this skill for MolMIM, NVIDIA's BioNeMo NIM microservice for small-molecule latent-space generation and optimizat…

nvidia-bionemo/bionemo-agent-toolkit

206

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rfdiffusion-nim Run RFDiffusion protein backbone design via NVIDIA NIM. Use for de novo protein backbones, motif scaffolding, binder …

nvidia-bionemo/bionemo-agent-toolkit

206

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evo2-nim Generate and analyze DNA sequences using NVIDIA's Evo 2 BioNeMo NIM microservice. Use for Evo2/Evo 2, DNA generation,…

nvidia-bionemo/bionemo-agent-toolkit

205

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proteinmpnn-nim Run ProteinMPNN inverse folding via NVIDIA NIM to design protein sequences for a target backbone. Use for ProteinMPNN…

nvidia-bionemo/bionemo-agent-toolkit

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msa-structure-prediction-pipeline NOTE: your protein sequence and the retrieved MSA alignment are transmitted to external NVIDIA-hosted APIs (health.ap…

nvidia-bionemo/bionemo-agent-toolkit

199

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nvmolkit-usage Write code that calls the installed nvMolKit Python API for GPU-accelerated, batched RDKit-style operations - Morgan …

nvidia-bionemo/bionemo-agent-toolkit

198

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complexa-design End-to-end Proteina-Complexa design pipeline driver. Use when the user wants to "design a binder", "design binders fo…

nvidia-bionemo/bionemo-agent-toolkit

196

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genomics-workflow-acceleration Use when accelerating existing genomics workflows with NVIDIA Parabricks, improving runtime or price/performance, con…

nvidia-bionemo/bionemo-agent-toolkit

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complexa-evaluate-pdbs Standalone evaluation of an existing PDB directory with Proteina-Complexa. Use when the user wants to "evaluate PDB f…

nvidia-bionemo/bionemo-agent-toolkit

193

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complexa-setup First-time setup, environment configuration, and model-weight installation for Proteina-Complexa. Reach for this skil…

nvidia-bionemo/bionemo-agent-toolkit

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openfold2-nim Use this skill for OpenFold2, NVIDIA's BioNeMo NIM microservice for monomer protein structure prediction. Invoke when…

nvidia-bionemo/bionemo-agent-toolkit

192

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kermt-embed Extract per-molecule embeddings from any encoder-bearing KERMT checkpoint (grover_base / cmim / hybrid / finetuned). …

nvidia-bionemo/bionemo-agent-toolkit

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parabricks Route NVIDIA Parabricks pbrun tools, assess GPU/runtime readiness, and provide version-aware command guidance for FAS…

nvidia-bionemo/bionemo-agent-toolkit

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complexa-target Use this skill whenever the user wants to add, register, edit, list, show, or validate a Proteina-Complexa design tar…

nvidia-bionemo/bionemo-agent-toolkit

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kermt-infer Run predictions with a finetuned KERMT checkpoint on a SMILES-only CSV. The skill validates that the input ckpt has t…

nvidia-bionemo/bionemo-agent-toolkit

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complexa-sweep Use this skill whenever the user wants to run a parameter sweep over a Proteina-Complexa design pipeline — cartesian-…

nvidia-bionemo/bionemo-agent-toolkit

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kermt-finetune Finetune a pretrained KERMT encoder on a labeled CSV. The skill validates the input checkpoint (must be a pretrain ck…

nvidia-bionemo/bionemo-agent-toolkit

185

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kermt-monitor Check progress for a detached KERMT run (pretrain, finetune, or any kermt_run_detached invocation). Reads run.json, q…

nvidia-bionemo/bionemo-agent-toolkit

185

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kermt-setup Bootstrap the KERMT agent environment — verify host docker + nvidia-container-toolkit, build the kermt:latest image f…

nvidia-bionemo/bionemo-agent-toolkit

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kermt-pretrain-scratch Pretrain a fresh KERMT model from scratch on a user-provided corpus. Builds a new vocabulary from the corpus, instant…

nvidia-bionemo/bionemo-agent-toolkit

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kermt-continue-pretrain Continue pretraining from an existing KERMT checkpoint. The skill validates the user's checkpoint and pretrain CSV, p…

nvidia-bionemo/bionemo-agent-toolkit

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cuequivariance Define custom groups (Irrep subclasses), build segmented tensor products with CG coefficients, create equivariant pol…

nvidia-bionemo/bionemo-agent-toolkit

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kermt-add-cmim-pretrain Convert a grover_base checkpoint (encoder-only or encoder + vocab heads) into a hybrid checkpoint by adding a randoml…

nvidia-bionemo/bionemo-agent-toolkit

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complexa-slurm Launch Proteina-Complexa pipelines on a remote SLURM cluster — binder search, LaProteina monomer design, or multi-nod…

nvidia-bionemo/bionemo-agent-toolkit

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protein-binder-design Orchestrate an end-to-end de novo protein binder design campaign against a protein target by composing BioNeMo NIM sk…

nvidia-bionemo/bionemo-agent-toolkit

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complexa-binder-design Run a complete protein binder design campaign with NVIDIA Proteina-Complexa: resolve a target structure and hotspots …

nvidia-bionemo/bionemo-agent-toolkit

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