521 件 ・ 関連度順
概要と使いどころ
Fetch 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) Extract specific chains or domains, (5) Get structure metadata. For sequence lookup, use uniprot. For binder design workflow, use binder-design.
日本語の概要は準備中です。原文の説明を表示しています。
Boltz-1 / Boltz-2 structure prediction for proteins, complexes, and ligand-aware validation. Use this skill when: (1) Predicting protein complex structures, (2) Validating designed binders, (3) Need open-source alternative to AF2, (4) Predicting protein-ligand complexes, (5) Using local GPU resources. For QC thresholds, use protein-design-qc. For AlphaFold2 prediction, use alphafold2-multimer. For Chai prediction, use chai1-structure-prediction.
日本語の概要は準備中です。原文の説明を表示しています。
First-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 authentication errors occur, (4) User asks how to get started or set up the environment, (5) biomodals directory is missing or tools aren't working.
日本語の概要は準備中です。原文の説明を表示しています。
Guidance 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, (4) Choosing between SPR vs BLI platforms.
日本語の概要は準備中です。原文の説明を表示しています。
Binder design tool selection and workflow routing guidance. Use this skill when: (1) Deciding between BoltzGen, BindCraft, or RFdiffusion, (2) Planning a binder design campaign, (3) Understanding trade-offs between different approaches, (4) Selecting tools for specific target types. For specific tool parameters, use the individual tool skills (boltzgen, bindcraft, rfdiffusion, etc.).
日本語の概要は準備中です。原文の説明を表示しています。
Workflow for read alignment, sorting, indexing, mapping statistics, and downstream-ready alignment artifacts.
日本語の概要は準備中です。原文の説明を表示しています。
Solubility-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 propensity, (4) Need high-yield expression, (5) Avoiding inclusion body formation. For standard design, use proteinmpnn. For ligand-aware design, use ligandmpnn.
日本語の概要は準備中です。原文の説明を表示しています。
Cell-free protein synthesis (CFPS) planning and optimization guidance. Use when: (1) Planning CFPS experiments, (2) Troubleshooting low yield or aggregation, (3) Optimizing DNA template design for CFPS, (4) Expressing difficult proteins (disulfide-rich, toxic, membrane).
日本語の概要は準備中です。原文の説明を表示しています。
Workflow for orthology, synteny, ancestral reconstruction, and evolutionary comparison across genomes.
日本語の概要は準備中です。原文の説明を表示しています。
Quality 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 pLDDT, ipTM, PAE, (3) Checking sequence liabilities (cysteines, deamidation, polybasic clusters), (4) Creating multi-stage filtering pipelines, (5) Computing PyRosetta interface metrics (dG, SC, dSASA), (6) Checking biophysical properties (instability, GRAVY, pI), (7) Ranking designs with composite scoring. This skill provides research-backed thresholds from binder design competitions and published benchmarks.
日本語の概要は準備中です。原文の説明を表示しています。
Binder 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, (3) Comparing AF2/AF3/Boltz predictions, (4) Predicting binding success rates, (5) Need better ranking than ipTM or iPAE. For structure prediction, use chai or alphafold. For QC thresholds, use protein-qc.
日本語の概要は準備中です。原文の説明を表示しています。
Goal-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) Assessing campaign health and pass rates, (4) Diagnosing why designs are failing QC, (5) Estimating time, cost, and expected yields, (6) Selecting between design tools for a specific target. This skill orchestrates the other protein design tools. For individual tool parameters, use the specific tool skills.
日本語の概要は準備中です。原文の説明を表示しています。
All-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 diffusion (not just backbone), (4) Require precise binding geometries, (5) Using YAML-based configuration. For backbone-only generation, use rfdiffusion. For sequence-only design, use proteinmpnn. For structure validation, use boltz.
日本語の概要は準備中です。原文の説明を表示しています。
Guidance 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 trade-offs between different approaches, (4) Selecting tools for specific target types. For specific tool parameters, use the individual tool skills (boltzgen, bindcraft, rfdiffusion, etc.).
日本語の概要は準備中です。原文の説明を表示しています。
Validate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed sequences fold correctly, (2) Predicting binder-target complex structures, (3) Calculating confidence metrics (pLDDT, pTM, ipTM), (4) Self-consistency validation of designs, (5) Multi-chain complex prediction with AlphaFold-Multimer. For faster single-chain prediction, use esm. For QC thresholds, use protein-qc.
日本語の概要は準備中です。原文の説明を表示しています。
Workflow for RNA modification analysis such as m6A peak calling, differential modification, and transcript-level visualization.
日本語の概要は準備中です。原文の説明を表示しています。
Guidance 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) Expressing difficult proteins (disulfide-rich, toxic, membrane).
日本語の概要は準備中です。原文の説明を表示しています。
ESM2 protein language model for sequence scoring, embeddings, and plausibility checks. Use this skill when: (1) Computing pseudo-log-likelihood (PLL) scores, (2) Getting protein embeddings for clustering, (3) Filtering designs by sequence plausibility, (4) Zero-shot variant effect prediction, (5) Analyzing sequence-function relationships. For structure prediction, use chai1-structure-prediction or boltz-structure-prediction. For QC thresholds, use protein-design-qc.
日本語の概要は準備中です。原文の説明を表示しています。
End-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, (4) Planning compute resources and timelines, (5) Integrating multiple design tools. For tool selection, use binder-design. For QC thresholds, use protein-qc.
日本語の概要は準備中です。原文の説明を表示しています。
Workflow for regulatory network inference, regulon scoring, perturbation-aware comparison, and network visualization.
日本語の概要は準備中です。原文の説明を表示しています。
Workflow for de novo assembly, scaffolding, polishing, contamination review, and assembly QC.
日本語の概要は準備中です。原文の説明を表示しています。
Workflow for nanopore or PacBio long-read QC, alignment, polishing, methylation-aware analysis, and structural variant discovery.
日本語の概要は準備中です。原文の説明を表示しています。
Workflow for predictive modeling, biomarker discovery, survival modeling, and explainability over omics-derived features.
日本語の概要は準備中です。原文の説明を表示しています。
Workflow for methylation alignment or calling, DMR analysis, methylation QC, and locus-level interpretation.
日本語の概要は準備中です。原文の説明を表示しています。