「scaffold」の検索結果

Orchestrates an end-to-end de novo genome assembly project, routing each step to the right genome-assembly skill rather than restating it. Profiles the genome first (k-mer spectrum -> size, heterozygosity, ploidy), QCs reads, chooses an assembly path by data type (SPAdes for Illumina, Flye for noisy long reads, hifiasm for HiFi, metaFlye for communities), polishes only when needed, decontaminates, scaffolds with Hi-C, and finishes with three-axis QC (contiguity + completeness + correctness). Use when assembling a genome from raw reads and deciding which assembler, whether to polish, and how to prove the result is good.

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Publication-quality molecular visualization. 2D structure drawings (PNG/SVG), molecule grids with property annotations, scaffold highlighting, protein-ligand interaction diagrams, and interactive 3D views.

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Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.

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Performs ML-based protein-ligand pose prediction and scoring using DiffDock-L (diffusion-based), Boltz-1 / Boltz-2 (foundation model with affinity), Chai-1, AlphaFold3 ligand, EquiBind, TANKBind, NeuralPLexer, and hybrid workflows (DiffDock pose + GNINA rescore + PoseBusters QC). Explicit handling of when ML beats classical docking, when classical beats ML, the PB-invalid pose problem, and rescoring as the standard production hybrid. Use when modern docking is needed: foundation-model ligand-pose prediction, AI rescoring of classical poses, or scaffold-hopping in cross-docking scenarios.

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Builds QSAR / QSPR models using chemprop D-MPNN, MolFormer, Uni-Mol, ChemBERTa, random forest baselines, and Gaussian processes with explicit handling of OECD 5 principles, applicability domain (kNN, leverage, conformal prediction, Mahalanobis), scaffold-balanced splits, ensemble uncertainty, calibration (Platt, isotonic), feature importance (SHAP, atomic attribution), and prospective validation. Use when building target-specific predictive models from in-house bioassay data, ADMET endpoints, or selectivity profiles.

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De novo molecule generation for drug discovery. Scaffold-based analog enumeration, fragment growing/linking, structure-based design, multi-objective optimization, and drug-likeness filtering.

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Searches molecular libraries for substructure matches using SMARTS patterns with explicit handling of recursive SMARTS, ring membership, aromaticity dialect, vector binding, atom map indices, and reactive/PAINS/REOS/Brenk/Aldridge filter catalogs. Use when filtering compounds by pharmacophore features, functional groups, scaffold matches, or screening for assay-interference / structural alerts.

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Performs molecular similarity searching using Tanimoto, Tversky, Dice, and cosine coefficients on bit/count fingerprints with explicit choice rules for symmetric vs asymmetric measures, scaffold-hopping vs lead-optimization regimes, activity-cliff diagnosis, and large-library nearest-neighbor methods (BulkTanimoto, Annoy MHFP6, USRCAT). Use when ranking compounds by structural resemblance to a query, clustering libraries, finding analogs, or diagnosing activity cliffs.

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Builds and applies 3D pharmacophore models using RDKit Pharm3D, the apo2ph4 receptor-based workflow (Heider et al 2022/2023 J Chem Inf Model 63:147-158), Pharmer / Pharmit (search), and PharmacoForge (diffusion-based generation, Flynn et al 2025 Front Bioinform), covering ligand-based pharmacophore (from active set alignment) and receptor-based pharmacophore (from binding pocket geometry). Explicit handling of feature types, geometric tolerances, partial matching, and pharmacophore-based virtual screening. Use when identifying scaffold-hopping candidates, building shape-and-feature search queries, or transferring SAR across chemotypes.

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Continues Charted Coding work for a PR by routing to scaffold, red, or green based on design doc progress. Use when resuming work on a PR, continuing TDD after a break, or when the user invokes charted continue with a design doc and PR number.

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Writes work-in-progress code and tests based on design doc

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Bootstrap a complete .github/workflows/ set for a new project: CI (build/test/lint), CD (workflow_dispatch with env choice + OIDC + ECR), security-scan (gitleaks + dependency scan + CodeQL), and optional database-migration. Use this skill when the user wants to add GitHub Actions CI/CD to a project that does not already have it, or when they want to add missing workflows alongside existing ones.

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This skill should be used when the user says "add a billing agent", "add a bookkeeping agent", "set up a support tier-1 agent", "add a recruiting agent", "add a compliance agent", "add a CRM agent", "add a contracts agent", "add an analytics agent", "add a marketing email agent", "add a CMS agent", "scaffold a function-specific agent", or wants to add a single business-function agent backed by a verified-write MCP integration. Each agent ships with explicit scope, "what this will NOT do" constraints, and recommended human-in-the-loop checkpoints.

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Scaffolds a complete .NET solution following Clean Architecture principles with proper layer separation (API, Application, Domain, Infrastructure). Creates project structure, dependency injection setup, and cross-cutting concerns configuration.

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Use to start a new product on Cradle or to add the Cradle skeleton to an existing repository — writes cradle.json, the project-facts instruction (.apm/instructions/project.instructions.md), documents/{ddd,ai-notes,infra-design,codebase} templates, CI, and a compiling Lean executable-spec scaffold with a minimal example domain, mockup and CLI.

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init 直後またはスタック変更時に実行。静的チェック基準カタログ（A1〜F2）を判断基準に、プロダクトへ決定的チェック（Lint / 静的解析）を選択・配線・補完し、カバレッジマップ（採否台帳）と `lint:all` コマンドを整備する。

Generate Python/pytest unit test skeletons from specifications.

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Generate Vue.js component test skeletons (Vue Test Utils) from specifications.

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Generate Remix loader/action and route component test skeletons.

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Generate generic React component test skeletons (RTL) from specifications.

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Generate React/Next.js component test skeletons (RTL) from specifications.

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Generate PHP/Laravel (PHPUnit) test skeletons from specifications.

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Generate TypeScript unit test skeletons (Jest/Vitest) from specifications.

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Performs molecular similarity searching using Tanimoto, Tversky, Dice, and cosine coefficients on bit/count fingerprints with explicit choice rules for symmetric vs asymmetric measures, scaffold-hopping vs lead-optimization regimes, activity-cliff diagnosis, and large-library nearest-neighbor methods (BulkTanimoto, Annoy MHFP6, USRCAT). Use when ranking compounds by structural resemblance to a query, clustering libraries, finding analogs, or diagnosing activity cliffs.

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。