adaptyvbio/protein-design-skills
24 skills · 788 total installs
$npx skills add adaptyvbio/protein-design-skillsSkillInstalls
alphafoldValidate protein designs using AlphaFold2 structure prediction.protein-design-workflowEnd-to-end guidance for protein design pipelines. Use this skill when: (1) Starting a new protein design project, (2) Need step-by-step workflow guidance, (3)…proteinmpnnDesign protein sequences using ProteinMPNN inverse folding. Use this skill when: (1) Designing sequences for RFdiffusion backbones, (2) Redesigning existing…pdbFetch and analyze protein structures from RCSB PDB. Use this skill when: (1) Need to download a structure by PDB ID, (2) Search for similar structures, (3)…binder-designGuidance for choosing the right protein binder design tool. Use this skill when: (1) Deciding between BoltzGen, BindCraft, or RFdiffusion, (2) Planning a…cell-free-expressionGuidance for cell-free protein synthesis (CFPS) optimization. Use when: (1) Planning CFPS experiments, (2) Troubleshooting low yield or aggregation, (3)…protein-qcQuality control metrics and filtering thresholds for protein design.campaign-managerGoal-oriented binder design campaign planning and health assessment.chaiStructure prediction using Chai-1, a foundation model for molecular structure.ipsaeBinder design ranking using ipSAE (interprotein Score from Aligned Errors).uniprotAccess UniProt for protein sequence and annotation retrieval. Use this skill when: (1) Looking up protein sequences by accession, (2) Finding functional…boltzStructure prediction using Boltz-1/Boltz-2, an open biomolecular structure predictor.binding-characterizationGuidance for SPR and BLI binding characterization experiments.foldseekStructure similarity search with Foldseek. Use this skill when: (1) Finding similar structures in PDB/AFDB databases, (2) Structural homology search, (3)…boltzgenAll-atom protein design using BoltzGen diffusion model. Use this skill when: (1) Need side-chain aware design from the start, (2) Designing around small…esmESM protein language models for embeddings, sequence scoring, structure prediction, and binder design.rfdiffusionGenerate protein backbones using RFdiffusion, a diffusion-based generative model for de novo protein structure generation.bindcraftEnd-to-end binder design using BindCraft hallucination. Use this skill when: (1) Designing protein binders with built-in AF2 validation, (2) Running…ligandmpnnLigand-aware protein sequence design using LigandMPNN. Use this skill when: (1) Designing sequences around small molecules, (2) Enzyme active site design, (3)…setupFirst-time setup for protein design tools. Use this skill when: (1) User is new and hasn't run any tools yet, (2) Commands fail with "file not found" or…solublempnnSolubility-optimized protein sequence design using SolubleMPNN. Use this skill when: (1) Designing for E.germinalDe novo antibody and nanobody (VHH) design with Germinal. Use this skill when: (1) Designing epitope-targeted nanobodies or scFvs, (2) Needing CDR design on a…mosaicMulti-objective, gradient-based protein binder design with Mosaic.protenixStructure prediction with Protenix, an open AlphaFold3 reproduction.