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SkillsMP 已收集 NVIDIA-BioNeMo/bionemo-agent-toolkit 中的 35 个 Skill。打开任一 Skill 可查看来源和详情。
已展示 35 / 35 个已收集 Skill。
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…
原文语言：英语
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,…
原文语言：英语
Run a complete protein binder design campaign with NVIDIA Proteina-Complexa: resolve a target structure and hotspots from a name/sequence/PDB, co-design binder sequence+structure with reward-guided test-time search (best-of-n, beam search, FK steering, MCTS),…
原文语言：英语
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…
原文语言：英语
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…
原文语言：英语
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…
原文语言：英语
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…
原文语言：英语
Orchestrate an end-to-end de novo protein binder design campaign against a protein target by composing BioNeMo NIM skills. Use for binder design, minibinder design, de novo binders, RFdiffusion + ProteinMPNN + Boltz2/OpenFold3 pipelines,…
原文语言：英语
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, omit_AAs, sampling temperature, soluble model, hosted NVIDIA…
原文语言：英语
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…
原文语言：英语
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…
原文语言：英语
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…
原文语言：英语
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…
原文语言：英语
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…
原文语言：英语
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…
原文语言：英语
NOTE: molecule and target inputs and your NGC_API_KEY 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…
原文语言：英语
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…
原文语言：英语
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…
原文语言：英语
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…
原文语言：英语
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…
原文语言：英语
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…
原文语言：英语
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…
原文语言：英语
End-to-end Proteina-Complexa design pipeline driver. Use when 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…
原文语言：英语
Standalone evaluation of an existing PDB directory with Proteina-Complexa. Use when the user wants to "evaluate PDB files", "re-fold these designs", "compute interface pAE", "compute i_pLDDT for a folder", "run AF2 / RF3 / ESMFold on my designs", "score…
原文语言：英语
First-time setup, environment configuration, and model-weight installation for Proteina-Complexa. Reach for this skill whenever the user says "set up complexa", "install complexa", "configure my environment file", "first-time setup", "what models do I have…
原文语言：英语
Use this skill whenever the user wants to run a parameter sweep over a Proteina-Complexa design pipeline — cartesian-product hyperparameter scans, Pareto search over generation/reward/evaluation knobs, or any "compare configurations" workflow. Trigger phrases…
原文语言：英语
Use this skill whenever the user wants to add, register, edit, list, show, or validate a Proteina-Complexa design target for any pipeline — protein binder (default), ligand binder, or AME / enzyme scaffolding. Triggers include "add a target", "define a new…
原文语言：英语
Convert a grover_base checkpoint (encoder-only or encoder + vocab heads) into a hybrid checkpoint by adding a randomly-initialized cMIM decoder + latent_dist, then continue pretraining on the user's corpus as hybrid (vocab + contrast). Effectively…
原文语言：英语
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 pretrain_ddp.py inside the kermt container (detached for long runs).…
原文语言：英语
Extract per-molecule embeddings from any encoder-bearing KERMT checkpoint (grover_base / cmim / hybrid / finetuned). Writes one .npy per readout type (atom_from_atom, bond_from_atom, atom_from_bond, bond_from_bond) plus canonical_smiles.npy and validity.npy.…
原文语言：英语
Finetune a pretrained KERMT encoder on a labeled CSV. The skill validates the input checkpoint (must be a pretrain ckpt — grover_base / cmim / hybrid), validates the labeled CSV, prepares the data (clean + features + optional split), then launches main.py…
原文语言：英语
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 + rdkit_2d features),…
原文语言：英语
Check progress for a detached KERMT run (pretrain, finetune, or any kermt_run_detached invocation). Reads run.json, queries docker for container state, tails the pretrain/finetune log, and parses progress lines (epoch, step, val loss).
原文语言：英语
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 pretrain_ddp.py inside the kermt container (detached for long runs). Unlike…
原文语言：英语
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;…
原文语言：英语