NVIDIA-BioNeMo

NVIDIA-BioNeMo/bionemo-agent-toolkit

Plugin Claude Code

Plugin marketplace listing 1 plugin: bionemo-agent-toolkit.

NVIDIA-BioNeMo/bionemo-agent-toolkit

Skill Claude CodeCodex

Define custom groups (Irrep subclasses), build segmented tensor products with CG coefficients, create equivariant polynomials and IrDictPolynomials, and use built-in descriptors (linear, tensor products, spherical harmonics). Use when working with cuequivariance group theory, irreps, or segmented polynomials.

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

Write code that calls the installed nvMolKit Python API for GPU-accelerated, batched RDKit-style operations - Morgan fingerprints, Tanimoto/cosine similarity, ETKDG conformer embedding, MMFF/UFF optimization, TFD, conformer RMSD, Butina clustering, and substructure search. Use when the user is importing nvmolkit.…

NVIDIA-BioNeMo/bionemo-agent-toolkit

Skill Claude CodeCodex

Route NVIDIA Parabricks pbrun tools, assess GPU/runtime readiness, and provide version-aware command guidance for FASTQ/BAM processing, RNA-seq, variant calling, BAM QC, and GVCF workflows. Do NOT use for inspecting or accelerating whole pipelines — use genomics-workflow-acceleration.

NVIDIA-BioNeMo/bionemo-agent-toolkit

Skill Claude CodeCodex

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 CodeCodex

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 CodeCodex

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 CodeCodex

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 CodeCodex

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 CodeCodex

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 CodeCodex

Use this skill for MolMIM, NVIDIA's BioNeMo NIM microservice for small-molecule latent-space generation and optimization. Invoke for MolMIM, molecular embeddings, hidden states, latent decoding, sampling around a seed SMILES, CMA-ES guided molecule generation, QED or plogP optimization, hosted NVIDIA API calls, or…

NVIDIA-BioNeMo/bionemo-agent-toolkit

Skill Claude CodeCodex

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 CodeCodex

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 CodeCodex

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 CodeCodex

Run ProteinMPNN inverse folding via NVIDIA NIM to design protein sequences for a target backbone. Use for ProteinMPNN, inverse folding, sequence design, backbone redesign, fixed chains/residues, omitAAs, sampling temperature, soluble model, hosted NVIDIA API, local Docker, PDB input, and multi-FASTA output.

NVIDIA-BioNeMo/bionemo-agent-toolkit

Skill Claude CodeCodex

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…