nvidia-bionemo/bionemo-agent-toolkit
32 skills
$npx skills add nvidia-bionemo/bionemo-agent-toolkitSkillInstalls
alphafold_database_fetch_and_analyzeRetrieve and analyze AlphaFold predicted structures for a protein.boltz2-nimUse Boltz2 NIM for biomolecular structure prediction and binding affinity.complexa-binder-designRun a complete protein binder design campaign with NVIDIA Proteina-Complexa: resolve a target structure and hotspots from a name/sequence/PDB, co-design binder…complexa-designEnd-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…complexa-evaluate-pdbsStandalone evaluation of an existing PDB directory with Proteina-Complexa.complexa-setupFirst-time setup, environment configuration, and model-weight installation for Proteina-Complexa.complexa-sweepUse this skill whenever the user wants to run a parameter sweep over a Proteina-Complexa design pipeline — cartesian-product hyperparameter scans, Pareto…complexa-targetUse this skill whenever the user wants to add, register, edit, list, show, or validate a Proteina-Complexa design target for any pipeline — protein binder…cuEquivarianceDefine custom groups (Irrep subclasses), build segmented tensor products with CG coefficients, create equivariant polynomials and IrDictPolynomials, and use…diffdock-nimRun DiffDock molecular docking via NVIDIA NIM to predict small-molecule binding poses against protein targets.drug-discovery-pipelineRun a complete computational drug discovery pipeline using NVIDIA BioNeMo NIMs: generate drug-like molecules with GenMol, dock them to a protein target with…evo2-nimGenerate and analyze DNA sequences using NVIDIA's Evo 2 BioNeMo NIM microservice.genmol-nimGenerate novel drug-like molecules using the GenMol NIM microservice.genomics-workflow-accelerationUse when accelerating existing genomics workflows with NVIDIA Parabricks, improving runtime or price/performance, converting pipeline steps to GPUs, or…kermt-add-cmim-pretrainConvert a grover_base checkpoint (encoder-only or encoder + vocab heads) into a hybrid checkpoint by adding a randomly-initialized cMIM decoder + latent_dist,…kermt-continue-pretrainContinue pretraining from an existing KERMT checkpoint. The skill validates the user's checkpoint and pretrain CSV, prepares the data into shard/vocab/features…kermt-embedExtract per-molecule embeddings from any encoder-bearing KERMT checkpoint (grover_base / cmim / hybrid / finetuned).kermt-finetuneFinetune a pretrained KERMT encoder on a labeled CSV. The skill validates the input checkpoint (must be a pretrain ckpt — grover_base / cmim / hybrid),…kermt-inferRun predictions with a finetuned KERMT checkpoint on a SMILES-only CSV.kermt-monitorCheck progress for a detached KERMT run (pretrain, finetune, or any kermt_run_detached invocation).kermt-pretrain-scratchPretrain a fresh KERMT model from scratch on a user-provided corpus.kermt-setupBootstrap the KERMT agent environment — verify host docker + nvidia-container-toolkit, build the kermt:latest image from the repo's Dockerfile if it doesn't…molmim-nimUse this skill for MolMIM, NVIDIA's BioNeMo NIM microservice for small-molecule latent-space generation and optimization.msa-search-nimGenerate multiple sequence alignments (MSAs) for protein sequences using the ColabFold MSA-Search NIM.msa-structure-prediction-pipelineRun a complete protein structure prediction pipeline using NVIDIA BioNeMo NIMs: search for MSA alignments with MSA-Search (ColabFold), then predict the…nvMolKitWrite code that calls the installed nvMolKit Python API for GPU-accelerated, batched RDKit-style operations - Morgan fingerprints, Tanimoto/cosine similarity,…openfold2-nimUse this skill for OpenFold2, NVIDIA's BioNeMo NIM microservice for monomer protein structure prediction.openfold3-nimUse this skill for OpenFold3, NVIDIA's BioNeMo NIM microservice for biomolecular structure prediction.parabricksRoute NVIDIA Parabricks pbrun tools, assess GPU/runtime readiness, and provide version-aware command guidance for FASTQ/BAM processing, RNA-seq, variant…proteinmpnn-nimRun ProteinMPNN inverse folding via NVIDIA NIM to design protein sequences for a target backbone.rfdiffusion-nimRun RFDiffusion protein backbone design via NVIDIA NIM. Use for de novo protein backbones, motif scaffolding, binder design, hotspot residues, contigs syntax,…uniprot_databaseAccess protein metadata, function, taxonomy, and sequences across UniProtKB, UniParc, and UniRef.