adaptyvbio/protein-design-skills
24 skills · 786 total installs
$npx skills add adaptyvbio/protein-design-skillsSkillInstalls
alphafoldValidate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed sequences fold correctly, (2) Predicting binder-target complex structures, (3) Calculating proteinmpnnDesign protein sequences using ProteinMPNN inverse folding. Use this skill when: (1) Designing sequences for RFdiffusion backbones, (2) Redesigning existing protein sequences, (3) Fixing specific resipdbFetch 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) Prepare target for binder design, (4) Extracprotein-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) Understanding the full design pipeline, (binder-designGuidance for choosing the right protein binder design tool. Use this skill when: (1) Deciding between BoltzGen, BindCraft, or RFdiffusion, (2) Planning a binder design campaign, (3) Understanding tradcell-free-expressionGuidance for cell-free protein synthesis (CFPS) optimization. Use when: (1) Planning CFPS experiments, (2) Troubleshooting low yield or aggregation, (3) Optimizing DNA template design for CFPS, (4) Exprotein-qcQuality control metrics and filtering thresholds for protein design. Use this skill when: (1) Evaluating design quality for binding, expression, or structure, (2) Setting filtering thresholds for pLDDcampaign-managerGoal-oriented binder design campaign planning and health assessment. Use this skill when: (1) Planning a complete binder design campaign, (2) Converting high-level goals into runnable pipelines, (3) AchaiStructure prediction using Chai-1, a foundation model for molecular structure. Use this skill when: (1) Predicting protein-protein complex structures, (2) Validating designed binders, (3) Predicting pipsaeBinder design ranking using ipSAE (interprotein Score from Aligned Errors). Use this skill when: (1) Ranking binder designs for experimental testing, (2) Filtering BindCraft or RFdiffusion outputs, (3uniprotAccess UniProt for protein sequence and annotation retrieval. Use this skill when: (1) Looking up protein sequences by accession, (2) Finding functional annotations, (3) Getting domain boundaries, (4)boltzStructure prediction using Boltz-1/Boltz-2, an open biomolecular structure predictor. Use this skill when: (1) Predicting protein complex structures, (2) Validating designed binders, (3) Need open-soubinding-characterizationGuidance for SPR and BLI binding characterization experiments. Use when: (1) Planning binding kinetics experiments, (2) Troubleshooting poor/no binding signal, (3) Interpreting kinetic data artifacts,foldseekStructure similarity search with Foldseek. Use this skill when: (1) Finding similar structures in PDB/AFDB databases, (2) Structural homology search, (3) Database queries by 3D structure, (4) Finding 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 molecules or ligands, (3) Want all-atom diffusiesmESM protein language models for embeddings, sequence scoring, structure prediction, and binder design. Use this skill when: (1) Computing pseudo-log-likelihood (PLL) or mutation-effect scores, (2) GetrfdiffusionGenerate protein backbones using RFdiffusion, a diffusion-based generative model for de novo protein structure generation. Use this skill when: (1) Designing binder scaffolds for a target protein, (2)bindcraftEnd-to-end binder design using BindCraft hallucination. Use this skill when: (1) Designing protein binders with built-in AF2 validation, (2) Running production-quality binder campaigns, (3) Using diffligandmpnnLigand-aware protein sequence design using LigandMPNN. Use this skill when: (1) Designing sequences around small molecules, (2) Enzyme active site design, (3) Ligand binding pocket optimization, (4) MsetupFirst-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 "modal: command not found", (3) Modal authenticsolublempnnSolubility-optimized protein sequence design using SolubleMPNN. Use this skill when: (1) Designing for E. coli expression, (2) Optimizing solubility of designed proteins, (3) Reducing aggregation propgerminalDe 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 fixed framework, (3) Working on antibody-mosaicMulti-objective, gradient-based protein binder design with Mosaic. Use this skill when: (1) Composing several structure or sequence models into one design objective, (2) Optimizing binders against a cprotenixStructure prediction with Protenix, an open AlphaFold3 reproduction. Use this skill when: (1) Predicting complex structures with an AF3-class model, (2) Wanting an open alternative to AF3 alongside Bo