「molecules」の検索結果

Detects somatic mutations in circulating tumor DNA, treating low-VAF detection as a signal-versus-noise problem set by error suppression and molecules sampled, not by the choice of caller. Distinguishes de novo CALLING (scanning a panel for unknown variants, bounded by per-locus error and multiple testing) from tumor-informed DETECTION (tracking a pre-specified variant set, where panel integration reaches single-ppm). Covers VarDict and Mutect2 for de novo calling, UMI-aware callers, and a pysam-based known-variant VAF tracker, with matched-WBC subtraction as the mandatory defense against clonal hematopoiesis (the dominant false positive). Use when calling or tracking tumor mutations from plasma cfDNA, setting a VAF threshold, or deciding whether a low-VAF call is tumor versus CHIP.

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Reads, writes, and converts molecular file formats (SMILES, InChI, SDF V2000/V3000, MOL2, PDB, and BinaryCIF) using RDKit and Open Babel with rigorous handling of aromaticity perception, stereochemistry, implicit/explicit hydrogens, kekulization, and salt/fragment separation. Use when loading chemical libraries, debugging parse failures, or preparing molecules for downstream standardization, descriptor calculation, or docking.

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Designs novel molecules using REINVENT 4 (de novo, scaffold decoration, linker design, R-group, molecular optimization), MolMIM, Diffusion-based generators (DiGress, DiffSMol), and JT-VAE with explicit handling of multi-parameter optimization (MPO), goal-directed scoring functions, transfer/reinforcement/curriculum learning, synthetic accessibility scoring, and chemical space exploration vs exploitation. Use when designing new chemical matter against a target, decorating a scaffold, linking fragments, or optimizing a hit for multiple ADMET / activity properties simultaneously.

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Calculates molecular fingerprints (ECFP/Morgan, FCFP, MACCS, RDKit, AtomPair, TopologicalTorsion, Avalon, MAP4, MHFP6) and physicochemical descriptors (Lipinski, QED, TPSA, Crippen LogP, 3D shape) with explicit choice tables, bit vs count semantics, and partial-charge model selection. Use when featurizing molecules for similarity, QSAR, virtual screening, or ML, or selecting the correct fingerprint for a chemotype-aware task.

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Performs retrosynthetic planning using AiZynthFinder (template-based MCTS), maintained or version-pinned template-free models, ASKCOS, and emerging RetroSynFormer with explicit handling of route scoring, configurable MCTS rewards, building-block availability, and forward-prediction checks. Use when assessing synthetic feasibility of generated or selected molecules, planning multi-step syntheses, building synthesis-aware design pipelines, or screening libraries for retro-route feasibility.

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Multi-agent orchestrator for Claude Code. Use when user mentions gastown, gas town, gt commands, bd commands, convoys, polecats, crew, rigs, slinging work, multi-agent coordination, beads, hooks, molecules, workflows, the witness, the mayor, the refinery, the deacon, dogs, escalation, or wants to run multiple AI agents on projects simultaneously. Handles installation, workspace setup, work tracking, agent lifecycle, crash recovery, and all gt/bd CLI operations.

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Build or audit a design system including component library, design tokens, naming conventions, contribution model, and documentation. Use this skill whenever the user wants to build a design system, audit an existing system, define design tokens at the system level, structure a component library, or set up design system governance. Triggers on design system, component library, design tokens, atomic design, atoms, molecules, organisms, design system documentation, Storybook, Figma library, system governance, design contribution model. Also triggers when teams are inconsistent across products and a system is the answer.

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Query ChEMBL bioactivity database for drug-like molecules

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Query ChEMBL's bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.

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Read, write, and edit ChemDraw CDX/CDXML files with RDKit's rdkit.Chem.rdChemDraw plus direct XML editing, always paired with a rendered PNG. Parse molecules and reactions from .cdxml/.cdx, write structures with good 2D depiction, and hand-build or modify the parts RDKit cannot write: reaction arrows, plus signs, schemes/steps, and text/labels. Use for reaction schemes, synthesis routes, mechanisms, retrosynthesis, or SI figures. Critical: RDKit writes structures only — round-tripping a reaction through a Mol silently drops arrows and text; this skill shows the XML layer that preserves them. For pure molecular analysis (descriptors, fingerprints, SMARTS) use rdkit-cheminformatics; for multi-format 3D conversion use openbabel.

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Query the ZINC22 virtual compound library (CartBlanche API, billions of make-on-demand + purchasable molecules). Look up substances by ZINC ID, resolve a SMILES to its ZINC ID (exact match), inspect purchasability/catalogs, and assemble compound sets for docking. Property (MW/logP) filtering is done locally with RDKit. For bioactivity use chembl-database-bioactivity; for approved drugs use drugbank-database-access.

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PyTorch Geometric (PyG) for graph neural networks: node/graph classification, link prediction with GCN, GAT, GraphSAGE, GIN. Message passing, mini-batches, heterogeneous graphs, neighbor sampling, explainability. Supports molecules (QM9, MoleculeNet), social/knowledge graphs, 3D point clouds. For non-graph DL use PyTorch; for classical graph algorithms use NetworkX.

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Protein language models (ESM3, ESM C) for sequence generation, structure prediction, inverse folding, and embeddings. Design novel proteins, extract ML features, or fold sequences. Local GPU or EvolutionaryScale Forge API. Use AlphaFold for traditional folding; RDKit for small molecules.

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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.

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Ligand-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) Metal coordination site design, (5) Cofactor binding proteins. For standard protein design, use proteinmpnn. For solubility optimization, use solublempnn.

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Protocol for handling ambiguous decisions and missing/conflicting knowledge during code generation, design, and review. Ensures AI surfaces genuine judgment calls with structured options and stops on hallucination risk instead of silently assuming. Use when a decision has multiple valid approaches, when facts are missing or contradictory, when the user asks 'what should we do here?', 'is this a judgment call?', 'should I ask about this?', 'am I guessing here?', 'what are the tradeoffs?', or when deciding between two reasonable architectural or design options. Also composed by molecules to define how judgment calls and clarification requests are surfaced and resolved.

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Apply clean code principles when generating or modifying implementation code. Enforces function focus, naming clarity, complexity management, error handling, and self-documenting style. Use when the user mentions 'clean code', 'code quality', 'coding guidelines', or 'implementation quality'. Loaded automatically by the code-generating molecules (code-forge, refactor-safely, bug-fix). This skill governs the craft of writing individual code units -- not architecture (see architecture), not security posture (see secure-coding), not test structure (see test-quality), and not refactoring workflows (see refactor-safely).

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Apply security-conscious thinking when generating or modifying code. Enforces trust boundary awareness, input validation, injection prevention, secrets management, and defense-in-depth authorization. Use when generating code that handles user input, authentication, authorization, database queries, external APIs, or file operations, or when the user mentions 'security review', 'secure this', 'check for vulnerabilities', 'trust boundary', 'input validation', or 'OWASP'. Loaded automatically by the code-generating molecules (code-forge, refactor-safely, bug-fix). This skill governs the security posture of generated code -- not architecture (see architecture) and not code craft (see clean-code).

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Apply test quality principles when generating or reviewing test code. Enforces Arrange-Act-Assert structure, one behavior per test, assertion quality, test isolation, meaningful naming, and test data management. Use when writing tests, reviewing test code, or when the user mentions 'write tests', 'test this', 'test quality', 'test review', 'improve tests', or 'test structure'. Loaded automatically by the code-generating molecules (code-forge, refactor-safely, bug-fix). This skill governs the craft of writing individual test cases -- not what to test (that is driven by the code being implemented) but how to write tests that are reliable, readable, and maintainable.

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Validate any Lattice SKILL.md against all tier conventions — atoms, molecules, and refiners. Catches structural errors, broken cross-references, and convention violations before they reach the repo. If you just wrote or modified a Lattice skill file and haven't run this yet, run it now — manual review consistently misses the same categories of errors this skill is specifically designed to catch. Use when the user says 'validate this skill', 'check this skill', 'does this follow conventions', 'review this skill file', 'check my SKILL.md', or 'skill validate'. Reports PASS/FAIL with specific file-and-section findings and actionable fixes. Standalone — does not call other skills.

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Use when adding or reusing Flutter UI - organize widgets as atoms, molecules, and organisms in a shared library and never hand-roll a component that already exists

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Used to invoke the PXMeter tool for rigorous quality assessment of biomolecular structure prediction models (e.g., proteins, nucleic acids, small molecules). This skill covers single-sample CIF evaluations and large-scale dataset benchmarks, providing rich result parsing support. Trigger this skill when the user asks to "run PXMeter", "compare PDB/CIF evaluation results of different tools", "check benchmark scores", or asks "how accurate is the structure generated by the model".

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Craft CMS 5 front-end Twig development — atomic design, template architecture, components, Vite buildchain. Covers atoms/molecules/organisms, props/extends/block patterns, layout chains, view routing, content builders, image presets, Tailwind named-key collections, multi-brand CSS tokens, JavaScript boundaries (Alpine/DataStar/Vue, tabs, accordions), Vite asset loading, and front-end auth (login, registration, password reset, profiles).

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Query ChEMBL's bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.

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。