Turn any agent into a life science expert with NVIDIA BioNeMo skills.
NVIDIA-BioNeMo/bionemo-agent-toolkit
Skill Claude CodeCodex
Build and debug cuEquivariance irreps, custom Irrep subclasses, Clebsch-Gordan tensor products, and equivariant or segmented polynomials. Use for cuequivariance core descriptors and IrDictPolynomial layout or shape questions; framework execution requires the matching JAX or PyTorch API.
NVIDIA-BioNeMo/bionemo-agent-toolkit
Skill Claude CodeCodex
Use when accelerating existing genomics workflows with NVIDIA Parabricks, improving runtime or price/performance, converting pipeline steps to GPUs, or comparing CPU and GPU workflow outputs. Adds optional GPU steps in-place with runtime toggles (default off). Do NOT use for individual pbrun command routing — use…
NVIDIA-BioNeMo/bionemo-agent-toolkit
Skill Claude CodeCodex
Use when writing or debugging nvMolKit Python code for GPU-accelerated RDKit fingerprints, similarity, conformers, clustering, and molecular searches.
NVIDIA-BioNeMo/bionemo-agent-toolkit
Skill Claude CodeCodex
Plan NVIDIA Parabricks pbrun commands, translate CPU options and check runtime readiness. Use for individual tools, including planning-only questions.
NVIDIA-BioNeMo/bionemo-agent-toolkit
Skill Claude Code
Use Boltz2 NIM for biomolecular structure prediction and binding affinity. Invoke for Boltz2, protein structures, protein-ligand/DNA/RNA complexes, SMILES or CCD ligands, pIC50/IC50 affinity scoring, mmCIF output, hosted NVIDIA API calls, or local Docker deployment.
NVIDIA-BioNeMo/bionemo-agent-toolkit
Skill Claude Code
Run DiffDock molecular docking via NVIDIA NIM to predict small-molecule binding poses against protein targets. Use for DiffDock, molecular docking, ligand docking, blind docking, SMILES or SDF ligands, ranked poses, confidence scores, hosted NVIDIA API, or local Docker deployment.
NVIDIA-BioNeMo/bionemo-agent-toolkit
Skill Claude Code
Generate and analyze DNA sequences using NVIDIA's Evo 2 BioNeMo NIM microservice. Use for Evo2/Evo 2, DNA generation, genomic sequence generation, hosted generation, local Docker deployment, local forward passes, layer outputs, logits, sampled probabilities, and BioNeMo NIM workflows.
NVIDIA-BioNeMo/bionemo-agent-toolkit
Skill Claude Code
Generate novel drug-like molecules using the GenMol NIM microservice. Use for de novo generation, scaffold decoration, motif extension, lead optimization, SAFE notation, QED or LogP ranking, hosted NVIDIA API calls, or local Docker deployment. GenMol takes SAFE notation in the smiles field, not ordinary SMILES.
NVIDIA-BioNeMo/bionemo-agent-toolkit
Skill Claude Code
NOTE: molecule and target inputs and your NGCAPIKEY are transmitted to external NVIDIA-hosted API endpoints on every call. Use local NIM containers for confidential or proprietary data. Run a complete computational drug discovery pipeline using NVIDIA BioNeMo NIMs: generate drug-like molecules with GenMol, dock them…
NVIDIA-BioNeMo/bionemo-agent-toolkit
Skill Claude Code
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…
NVIDIA-BioNeMo/bionemo-agent-toolkit
Skill Claude Code
Generate multiple sequence alignments (MSAs) for protein sequences using the ColabFold MSA-Search NIM. Use for homolog search, UniRef30/ColabFold env searches, A3M or FASTA alignments, paired MSA search for complexes, PDB70 structural templates, hosted NVIDIA API calls, or local Docker deployment. For local…
NVIDIA-BioNeMo/bionemo-agent-toolkit
Skill Claude Code
Use this skill for OpenFold2, NVIDIA's BioNeMo NIM microservice for monomer protein structure prediction. Invoke whenever the user mentions OpenFold2, AlphaFold2-like monomer folding, protein sequence-to-structure prediction, A3M MSAs, mmCIF templates, hosted NVIDIA API calls, or local Docker deployment.
NVIDIA-BioNeMo/bionemo-agent-toolkit
Skill Claude Code
Use this skill for OpenFold3, NVIDIA's BioNeMo NIM microservice for biomolecular structure prediction. Invoke whenever the user mentions OpenFold3 or needs protein, protein-ligand, protein-DNA/RNA, or multi-chain complex prediction with the hosted NVIDIA API or local Docker NIM. Covers endpoint choice, auth, request…
NVIDIA-BioNeMo/bionemo-agent-toolkit
Skill Claude Code
Run RFDiffusion protein backbone design via NVIDIA NIM. Use for de novo protein backbones, motif scaffolding, binder design, hotspot residues, contigs syntax, diffusion steps, hosted NVIDIA API calls, local Docker deployment, and PDB backbone outputs for ProteinMPNN sequence design.
NVIDIA-BioNeMo/bionemo-agent-toolkit
Skill Claude CodeCodex
Convert a groverbase checkpoint (encoder-only or encoder + vocab heads) into a hybrid checkpoint by adding a randomly-initialized cMIM decoder + latentdist, then continue pretraining on the user's corpus as hybrid (vocab + contrast). Effectively kermt-continue-pretrain with a one-time ckpt-conversion step prepended.
NVIDIA-BioNeMo/bionemo-agent-toolkit
Skill Claude CodeCodex
Continue pretraining from an existing KERMT checkpoint. The skill validates the user's checkpoint and pretrain CSV, prepares the data into shard/vocab/features form, then launches pretrainddp.py inside the kermt container (detached for long runs). Auto-dispatches --pretrainmode based on the checkpoint type (groverbase…
NVIDIA-BioNeMo/bionemo-agent-toolkit
Skill Claude CodeCodex
Extract per-molecule embeddings from any encoder-bearing KERMT checkpoint (groverbase / cmim / hybrid / finetuned). Writes one .npy per readout type (atomfromatom, bondfromatom, atomfrombond, bondfrombond) plus canonicalsmiles.npy and validity.npy. Calls task/extractembeddings.py (which featurizes SMILES on the fly …
NVIDIA-BioNeMo/bionemo-agent-toolkit
Skill Claude CodeCodex
Finetune a pretrained KERMT encoder on a labeled CSV. The skill validates the input checkpoint (must be a pretrain ckpt — groverbase / cmim / hybrid), validates the labeled CSV, prepares the data (clean + features + optional split), then launches main.py finetune inside the kermt container (detached for hours-scale…
NVIDIA-BioNeMo/bionemo-agent-toolkit
Skill Claude CodeCodex
Run predictions with a finetuned KERMT checkpoint on a SMILES-only CSV. The skill validates that the input ckpt has task FFN heads (refuses pretrain ckpts with a redirect to kermt-finetune), validates the CSV, prepares the data (clean + rdkit2d features), then launches main.py predict inside the kermt container…
NVIDIA-BioNeMo/bionemo-agent-toolkit
Skill Claude CodeCodex
Check progress for a detached KERMT run (pretrain, finetune, or any kermtrundetached invocation). Reads run.json, queries docker for container state, tails the pretrain/finetune log, and parses progress lines (epoch, step, val loss).
NVIDIA-BioNeMo/bionemo-agent-toolkit
Skill Claude CodeCodex
Pretrain a fresh KERMT model from scratch on a user-provided corpus. Builds a new vocabulary from the corpus, instantiates the model architecture from defaults, and launches pretrainddp.py inside the kermt container (detached for long runs). Unlike kermt-continue-pretrain, no starting checkpoint is loaded — the model…
NVIDIA-BioNeMo/bionemo-agent-toolkit
Skill Claude CodeCodex
Bootstrap the KERMT agent environment — verify host docker + nvidia-container-toolkit, build the kermt:latest image from the repo's Dockerfile if it doesn't yet exist, and run a GPU smoke test inside the container. Every other kermt- skill depends on this; invoke it first.
NVIDIA-BioNeMo/bionemo-agent-toolkit
Skill Claude Code needs its repo
End-to-end Proteina-Complexa design pipeline driver. Reach for this skill whenever 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…
NVIDIA-BioNeMo/bionemo-agent-toolkit
Skill Claude Code needs its repo
Standalone evaluation of an existing PDB directory with Proteina-Complexa. Use this skill whenever 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"…
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: