nvidia-bionemo/bionemo-agent-toolkit

nvidia-bionemo/bionemo-agent-toolkit · library-skills/cuequivariance-jax/SKILL.md · Use when writing or debugging cuEquivariance JAX polynomials, irrep dictionaries, Flax NNX layers, or CPU/CUDA…

nvidia-bionemo/bionemo-agent-toolkit · library-skills/cuequivariance-torch/SKILL.md · Use when building or debugging cuEquivariance PyTorch tensor products or equivariant GNNs, especially CPU references…

nvidia-bionemo/bionemo-agent-toolkit · library-skills/cuequivariance/SKILL.md · Use when defining cuEquivariance groups and irreps, building equivariant tensor products, or validating segmented…

nvidia-bionemo/bionemo-agent-toolkit · library-skills/genomics-workflow-acceleration/SKILL.md · Use when accelerating existing genomics workflows with NVIDIA Parabricks, improving runtime or price/performance…

nvidia-bionemo/bionemo-agent-toolkit · library-skills/nvmolkit-usage/SKILL.md · Use when writing or debugging nvMolKit Python code for GPU-accelerated RDKit fingerprints, similarity, conformers…

nvidia-bionemo/bionemo-agent-toolkit · library-skills/parabricks/SKILL.md · Plan NVIDIA Parabricks pbrun commands, translate CPU options and check runtime readiness. Use for individual tools…

nvidia-bionemo/bionemo-agent-toolkit · nim-skills/boltz2-nim/SKILL.md · Use Boltz2 NIM for biomolecular structure prediction and binding affinity. Invoke for Boltz2, protein structures…

nvidia-bionemo/bionemo-agent-toolkit · nim-skills/diffdock-nim/SKILL.md · Run DiffDock molecular docking via NVIDIA NIM to predict small-molecule binding poses against protein targets. Use for…

nvidia-bionemo/bionemo-agent-toolkit · nim-skills/evo2-nim/SKILL.md · 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 · nim-skills/genmol-nim/SKILL.md · Generate novel drug-like molecules using the GenMol NIM microservice. Use for de novo generation, scaffold decoration…

nvidia-bionemo/bionemo-agent-toolkit · nim-skills/meta-skills/drug-discovery-pipeline/SKILL.md · NOTE: molecule and target inputs and your NGC_API_KEY are transmitted to external NVIDIA-hosted API endpoints on every…

nvidia-bionemo/bionemo-agent-toolkit · nim-skills/meta-skills/msa-structure-prediction-pipeline/SKILL.md · NOTE: your protein sequence and the retrieved MSA alignment are transmitted to external NVIDIA-hosted APIs…

nvidia-bionemo/bionemo-agent-toolkit · nim-skills/molmim-nim/SKILL.md · Use this skill for MolMIM, NVIDIA's BioNeMo NIM microservice for small-molecule latent-space generation and…

nvidia-bionemo/bionemo-agent-toolkit · nim-skills/msa-search-nim/SKILL.md · Generate multiple sequence alignments (MSAs) for protein sequences using the ColabFold MSA-Search NIM. Use for homolog…

nvidia-bionemo/bionemo-agent-toolkit · nim-skills/openfold2-nim/SKILL.md · Use this skill for OpenFold2, NVIDIA's BioNeMo NIM microservice for monomer protein structure prediction. Invoke…

nvidia-bionemo/bionemo-agent-toolkit · nim-skills/openfold3-nim/SKILL.md · Use this skill for OpenFold3, NVIDIA's BioNeMo NIM microservice for biomolecular structure prediction. Invoke whenever…

nvidia-bionemo/bionemo-agent-toolkit · nim-skills/proteinmpnn-nim/SKILL.md · Run ProteinMPNN inverse folding via NVIDIA NIM to design protein sequences for a target backbone. Sends user-provided…

nvidia-bionemo/bionemo-agent-toolkit · nim-skills/rfd4-proteina-nim/SKILL.md · Run RFD4-Proteina NIM for joint protein structure and sequence design, conditioned generation, and reward-guided search…

nvidia-bionemo/bionemo-agent-toolkit · nim-skills/rfdiffusion-nim/SKILL.md · Run RFDiffusion protein backbone design via NVIDIA NIM. Use for de novo protein backbones, motif scaffolding, binder…

nvidia-bionemo/bionemo-agent-toolkit · open-models-skills/codonfm/codonfm-embed/SKILL.md · Validate coding-sequence CSVs, extract public CodonFM/Encodon embeddings, and choose checkpoints for downstream…

nvidia-bionemo/bionemo-agent-toolkit · open-models-skills/codonfm/codonfm-finetune/SKILL.md · Fine-tune public CodonFM Encodon checkpoints on labeled coding-sequence or coding-variant data using LoRA, head-only…

nvidia-bionemo/bionemo-agent-toolkit · open-models-skills/codonfm/codonfm-score/SKILL.md · Validate, prepare, or run public CodonFM Encodon masked-codon variant scoring and review compatibility of its scoring…

nvidia-bionemo/bionemo-agent-toolkit · open-models-skills/codonfm/codonfm-setup/SKILL.md · Set up the public CodonFM v1 repository and download public Encodon checkpoints. Use for requests to build or launch…

nvidia-bionemo/bionemo-agent-toolkit · open-models-skills/kermt/kermt-add-cmim-pretrain/SKILL.md · Convert a grover_base checkpoint (encoder-only or encoder + vocab heads) into a hybrid checkpoint by adding a…

nvidia-bionemo/bionemo-agent-toolkit · open-models-skills/kermt/kermt-continue-pretrain/SKILL.md · Continue pretraining from an existing KERMT checkpoint. The skill validates the user's checkpoint and pretrain CSV…

nvidia-bionemo/bionemo-agent-toolkit · open-models-skills/kermt/kermt-embed/SKILL.md · Extract per-molecule embeddings from any encoder-bearing KERMT checkpoint (grover_base / cmim / hybrid / finetuned)…

nvidia-bionemo/bionemo-agent-toolkit · open-models-skills/kermt/kermt-finetune/SKILL.md · Finetune a pretrained KERMT encoder on a labeled CSV. The skill validates the input checkpoint (must be a pretrain ckpt…

nvidia-bionemo/bionemo-agent-toolkit · open-models-skills/kermt/kermt-infer/SKILL.md · Run predictions with a finetuned KERMT checkpoint on a SMILES-only CSV. The skill validates that the input ckpt has…

nvidia-bionemo/bionemo-agent-toolkit · open-models-skills/kermt/kermt-monitor/SKILL.md · Check progress for a detached KERMT run (pretrain, finetune, or any kermt_run_detached invocation). Reads run.json…

nvidia-bionemo/bionemo-agent-toolkit · open-models-skills/kermt/kermt-pretrain-scratch/SKILL.md · Pretrain a fresh KERMT model from scratch on a user-provided corpus. Builds a new vocabulary from the corpus…

nvidia-bionemo/bionemo-agent-toolkit · open-models-skills/kermt/kermt-setup/SKILL.md · Bootstrap the KERMT agent environment — verify host docker + nvidia-container-toolkit, build the kermt:latest image…

nvidia-bionemo/bionemo-agent-toolkit · open-models-skills/proteina-complexa/complexa-design/SKILL.md · End-to-end Proteina-Complexa design pipeline driver. Reach for this skill whenever the user wants to "design a binder"…

nvidia-bionemo/bionemo-agent-toolkit · open-models-skills/proteina-complexa/complexa-evaluate-pdbs/SKILL.md · Standalone evaluation of an existing PDB directory with Proteina-Complexa. Use this skill whenever the user wants to…

nvidia-bionemo/bionemo-agent-toolkit · open-models-skills/proteina-complexa/complexa-setup/SKILL.md · First-time setup, environment configuration, and model-weight installation for Proteina-Complexa. Reach for this skill…

nvidia-bionemo/bionemo-agent-toolkit · open-models-skills/proteina-complexa/complexa-sweep/SKILL.md · Use this skill whenever the user wants to run a parameter sweep over a Proteina-Complexa design pipeline —…

nvidia-bionemo/bionemo-agent-toolkit · open-models-skills/proteina-complexa/complexa-target/SKILL.md · Use this skill whenever the user wants to add, register, edit, list, show, or validate a Proteina-Complexa design…

nvidia-bionemo/bionemo-agent-toolkit · open-models-skills/rfd4-proteina/rfd4-proteina-annotated-cif/SKILL.md · Use when creating, inspecting, editing, or validating RFD4-Proteina annotated CIF inputs and conditioning with…

nvidia-bionemo/bionemo-agent-toolkit · open-models-skills/rfd4-proteina/rfd4-proteina-autoresearch/SKILL.md · Use when iterating RFD4-Proteina design waves with explicit rewards, parameter sweeps, budgets, and promotion decisions.

nvidia-bionemo/bionemo-agent-toolkit · open-models-skills/rfd4-proteina/rfd4-proteina-campaign/SKILL.md · Use when running RFD4-Proteina campaigns with provenance linking inputs, designs, oracle results, metrics, and passer…

nvidia-bionemo/bionemo-agent-toolkit · open-models-skills/rfd4-proteina/rfd4-proteina-commitment-curves/SKILL.md · Use for RFD4-Proteina commitment timing, partial-diffusion sweeps, parent-child correlations, and metric distributions.

nvidia-bionemo/bionemo-agent-toolkit · open-models-skills/rfd4-proteina/rfd4-proteina-evaluate/SKILL.md · Use when scoring existing RFD4-Proteina designs, aggregating metrics, adding custom metrics, or clustering diversity.

nvidia-bionemo/bionemo-agent-toolkit · open-models-skills/rfd4-proteina/rfd4-proteina-generate/SKILL.md · Use when generating RFD4-Proteina designs from annotated inputs with task, sampling, batch, and inline-metric choices.

nvidia-bionemo/bionemo-agent-toolkit · open-models-skills/rfd4-proteina/rfd4-proteina-package/SKILL.md · Use when packaging selected RFD4-Proteina designs, aligned refolds, measured metrics, and filters into a shareable TAR.

nvidia-bionemo/bionemo-agent-toolkit · open-models-skills/rfd4-proteina/rfd4-proteina-search/SKILL.md · Use when running RFD4-Proteina reward-guided beam search with chosen checkpoints, branching, metrics, and compute…

nvidia-bionemo/bionemo-agent-toolkit · open-models-skills/rfd4-proteina/rfd4-proteina-setup/SKILL.md · Use when installing or troubleshooting the RFD4-Proteina runtime, checkpoints, data paths, or GPU preflight.

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/boltz2-nim/SKILL.md · Use Boltz2 NIM for biomolecular structure prediction and binding affinity. Invoke for Boltz2, protein structures…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/codonfm-embed/SKILL.md · Validate coding-sequence CSVs, extract public CodonFM/Encodon embeddings, and choose checkpoints for downstream…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/codonfm-finetune/SKILL.md · Fine-tune public CodonFM Encodon checkpoints on labeled coding-sequence or coding-variant data using LoRA, head-only…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/codonfm-score/SKILL.md · Validate, prepare, or run public CodonFM Encodon masked-codon variant scoring and review compatibility of its scoring…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/codonfm-setup/SKILL.md · Set up the public CodonFM v1 repository and download public Encodon checkpoints. Use for requests to build or launch…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/complexa-binder-design/SKILL.md · Run a complete protein binder design campaign with NVIDIA Proteina-Complexa: resolve a target structure and hotspots…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/complexa-design/SKILL.md · End-to-end Proteina-Complexa design pipeline driver. Reach for this skill whenever the user wants to "design a binder"…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/complexa-evaluate-pdbs/SKILL.md · Standalone evaluation of an existing PDB directory with Proteina-Complexa. Use this skill whenever the user wants to…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/complexa-setup/SKILL.md · First-time setup, environment configuration, and model-weight installation for Proteina-Complexa. Reach for this skill…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/complexa-sweep/SKILL.md · Use this skill whenever the user wants to run a parameter sweep over a Proteina-Complexa design pipeline —…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/complexa-target/SKILL.md · Use this skill whenever the user wants to add, register, edit, list, show, or validate a Proteina-Complexa design…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/cuequivariance-jax/SKILL.md · Use when writing or debugging cuEquivariance JAX polynomials, irrep dictionaries, Flax NNX layers, or CPU/CUDA…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/cuequivariance-torch/SKILL.md · Use when building or debugging cuEquivariance PyTorch tensor products or equivariant GNNs, especially CPU references…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/cuequivariance/SKILL.md · Use when defining cuEquivariance groups and irreps, building equivariant tensor products, or validating segmented…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/diffdock-nim/SKILL.md · Run DiffDock molecular docking via NVIDIA NIM to predict small-molecule binding poses against protein targets. Use for…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/drug-discovery-pipeline/SKILL.md · NOTE: molecule and target inputs and your NGC_API_KEY are transmitted to external NVIDIA-hosted API endpoints on every…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/evo2-nim/SKILL.md · 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 · skills/bionemo-agent-toolkit/skills/genmol-nim/SKILL.md · Generate novel drug-like molecules using the GenMol NIM microservice. Use for de novo generation, scaffold decoration…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/genomics-workflow-acceleration/SKILL.md · Use when accelerating existing genomics workflows with NVIDIA Parabricks, improving runtime or price/performance…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/kermt-add-cmim-pretrain/SKILL.md · Convert a grover_base checkpoint (encoder-only or encoder + vocab heads) into a hybrid checkpoint by adding a…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/kermt-continue-pretrain/SKILL.md · Continue pretraining from an existing KERMT checkpoint. The skill validates the user's checkpoint and pretrain CSV…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/kermt-embed/SKILL.md · Extract per-molecule embeddings from any encoder-bearing KERMT checkpoint (grover_base / cmim / hybrid / finetuned)…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/kermt-finetune/SKILL.md · Finetune a pretrained KERMT encoder on a labeled CSV. The skill validates the input checkpoint (must be a pretrain ckpt…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/kermt-infer/SKILL.md · Run predictions with a finetuned KERMT checkpoint on a SMILES-only CSV. The skill validates that the input ckpt has…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/kermt-monitor/SKILL.md · Check progress for a detached KERMT run (pretrain, finetune, or any kermt_run_detached invocation). Reads run.json…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/kermt-pretrain-scratch/SKILL.md · Pretrain a fresh KERMT model from scratch on a user-provided corpus. Builds a new vocabulary from the corpus…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/kermt-setup/SKILL.md · Bootstrap the KERMT agent environment — verify host docker + nvidia-container-toolkit, build the kermt:latest image…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/molmim-nim/SKILL.md · Use this skill for MolMIM, NVIDIA's BioNeMo NIM microservice for small-molecule latent-space generation and…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/msa-search-nim/SKILL.md · Generate multiple sequence alignments (MSAs) for protein sequences using the ColabFold MSA-Search NIM. Use for homolog…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/msa-structure-prediction-pipeline/SKILL.md · NOTE: your protein sequence and the retrieved MSA alignment are transmitted to external NVIDIA-hosted APIs…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/nvmolkit-usage/SKILL.md · Use when writing or debugging nvMolKit Python code for GPU-accelerated RDKit fingerprints, similarity, conformers…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/openfold2-nim/SKILL.md · Use this skill for OpenFold2, NVIDIA's BioNeMo NIM microservice for monomer protein structure prediction. Invoke…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/openfold3-nim/SKILL.md · Use this skill for OpenFold3, NVIDIA's BioNeMo NIM microservice for biomolecular structure prediction. Invoke whenever…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/parabricks/SKILL.md · Plan NVIDIA Parabricks pbrun commands, translate CPU options and check runtime readiness. Use for individual tools…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/protein-binder-design/SKILL.md · Orchestrate an end-to-end de novo protein binder design campaign against a protein target by composing BioNeMo NIM…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/proteinmpnn-nim/SKILL.md · Run ProteinMPNN inverse folding via NVIDIA NIM to design protein sequences for a target backbone. Sends user-provided…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/rfd4-proteina-annotated-cif/SKILL.md · Use when creating, inspecting, editing, or validating RFD4-Proteina annotated CIF inputs and conditioning with…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/rfd4-proteina-autoresearch/SKILL.md · Use when iterating RFD4-Proteina design waves with explicit rewards, parameter sweeps, budgets, and promotion decisions.

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/rfd4-proteina-campaign/SKILL.md · Use when running RFD4-Proteina campaigns with provenance linking inputs, designs, oracle results, metrics, and passer…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/rfd4-proteina-commitment-curves/SKILL.md · Use for RFD4-Proteina commitment timing, partial-diffusion sweeps, parent-child correlations, and metric distributions.

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/rfd4-proteina-evaluate/SKILL.md · Use when scoring existing RFD4-Proteina designs, aggregating metrics, adding custom metrics, or clustering diversity.

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/rfd4-proteina-generate/SKILL.md · Use when generating RFD4-Proteina designs from annotated inputs with task, sampling, batch, and inline-metric choices.

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/rfd4-proteina-nim/SKILL.md · Run RFD4-Proteina NIM for joint protein structure and sequence design, conditioned generation, and reward-guided search…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/rfd4-proteina-package/SKILL.md · Use when packaging selected RFD4-Proteina designs, aligned refolds, measured metrics, and filters into a shareable TAR.

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/rfd4-proteina-search/SKILL.md · Use when running RFD4-Proteina reward-guided beam search with chosen checkpoints, branching, metrics, and compute…

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/rfd4-proteina-setup/SKILL.md · Use when installing or troubleshooting the RFD4-Proteina runtime, checkpoints, data paths, or GPU preflight.

nvidia-bionemo/bionemo-agent-toolkit · skills/bionemo-agent-toolkit/skills/rfdiffusion-nim/SKILL.md · Run RFDiffusion protein backbone design via NVIDIA NIM. Use for de novo protein backbones, motif scaffolding, binder…

nvidia-bionemo/bionemo-agent-toolkit · workflows/generative-protein-binder-design/complexa-binder-design/SKILL.md · Run a complete protein binder design campaign with NVIDIA Proteina-Complexa: resolve a target structure and hotspots…

nvidia-bionemo/bionemo-agent-toolkit · workflows/generative-protein-binder-design/protein-binder-design/SKILL.md · Orchestrate an end-to-end de novo protein binder design campaign against a protein target by composing BioNeMo NIM…