「discovery」の検索結果

Dereplicate a putative natural product and assign its chemical taxonomy. Use to answer "is [compound] a known natural product", "what microbe/organism produces [compound]", "what chemical class is [compound]", "dereplicate this metabolite (by formula/exact mass/InChIKey/SMILES)", or "classify this molecule into ChemOnt". Searches NPAtlas for known microbial natural products (producing organism + literature reference), assigns the ChemOnt kingdom→superclass→class→subclass hierarchy via ClassyFire, resolves systematic IUPAC names to structure via OPSIN, and cross-references identity in PubChem. NOT for general drug/compound identity or ADMET (use tooluniverse-chemical-compound-retrieval / tooluniverse-small-molecule-discovery) and NOT for metabolomics pathway/enrichment analysis (use tooluniverse-metabolomics skills).

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PyTorch-native graph neural networks for molecules and proteins. Use when building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reasoning. Best for custom model development, protein property prediction, retrosynthesis. For pre-trained models and diverse featurizers use deepchem; for benchmark datasets use pytdc.

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Compound-target-disease network construction and analysis for drug repurposing, polypharmacology discovery, and multi-target drug design. Uses STRING, BioGRID, ChEMBL, DGIdb, OMIM, OpenTargets. Use for off-target effect prediction, network-based drug repurposing, and identifying molecules with desired multi-target profile.

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Protein structure prediction from sequence. ESMFold-based, single GPU, no MSA needed. Predicts 3D structures with pLDDT confidence scores for drug discovery targets.

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GPCR receptor pharmacology — agonist/antagonist/inverse-agonist/biased-agonist classification, GPCRdb structural data, receptor-ligand binding analysis, antibody-target interface (SAbDab). Use for GPCR drug discovery, biased-agonism analysis, receptor subtype selectivity questions, and orthosteric vs allosteric pocket characterization.

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KEGG-based disease-drug-variant network research. Connects diseases to causal genes, drugs to molecular targets, and variants to pathways using KEGG's editorially curated databases (KEGG Disease, Drug, Network, Variant, Pathway). Use for drug repurposing via shared pathways, mechanistic disease-gene-drug networks, and pathway-based target discovery. Distinguishes direct (binding) vs indirect (pathway co-membership) drug-target relationships.

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Transform GWAS signals into drug targets and repurposing opportunities. Connects GWAS-significant loci to causal genes via fine-mapping/eQTL, then to druggable proteins via DGIdb/OpenTargets, then to existing drugs via ChEMBL. Use for GWAS-to-target hypothesis generation, druggable-fraction analysis of disease loci, and human-genetics-validated drug-repurposing prioritization.

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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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Interpretable ADMET analysis with mechanistic reasoning. Maps liabilities to structural causes and biological pathways. Based on CoTox (Park 2025) and DrugR (Liu 2026).

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Hybrid ML + physics binding affinity prediction. Empirical scoring, MM/GBSA rescoring, multi-method consensus, and batch virtual screening for protein-ligand complexes.

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Retrieve structurally similar compounds with known properties from ChEMBL/ZINC to ground predictions and inform optimization. Based on MolRAG (Xian 2025, ACL).

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Multi-method binding pocket detection and druggability assessment. Grid-based, fpocket, and P2Rank detection with druggability scoring, visualization, and cross-structure comparison.

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Iterative lead optimization with analyze-reason-generate-verify-evaluate loop. Paper-backed (MT-Mol, DrugR, MultiMol).

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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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Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurization options and MoleculeNet benchmarks. Best for quick experiments with pre-trained models, diverse molecular representations. For graph-first PyTorch workflows use torchdrug; for benchmark datasets use pytdc.

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Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms.

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Decision-grade statistical analysis for metabolomics intensity tables. Covers transformation and scaling (Pareto vs unit-variance as a hidden hypothesis), unsupervised structure (PCA/HCA for QC), permutation-validated PLS-DA/OPLS-DA (R2 vs Q2, double CV, VIP as heuristic), univariate testing (Welch/Mann-Whitney/ANOVA/LMM with covariate adjustment), and dependence-aware multiple testing. Use when testing which metabolites differ, building or validating a discriminant model, choosing a scaling, or correcting many correlated tests. For sample-wise normalization/drift correction see metabolomics/normalization-qc; for ML classifiers and selection-inside-CV leakage see machine-learning/biomarker-discovery and machine-learning/model-validation; for pathway interpretation see metabolomics/pathway-mapping; for design/power/multiplicity regime see experimental-design/multiple-testing.

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Product manager for PRD creation and requirements discovery. Use when the user asks to talk to Nicole or requests the product manager.

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Research customer pain points, trends, and competitors through the OMA market engine. Use for market discovery or voice-of-customer analysis.

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This skill should be used when conducting a scored agent-native architecture review. It launches 8 parallel sub-agents to audit action parity, context injection, CRUD completeness, capability discovery, and prompt-native features.

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Audit and improve website readiness for AI agents using the Cloudflare "Is It Agent Ready?" scanner (isitagentready.com). Covers scanning via API, interpreting results, generating implementation prompts, and fixing every check. Use when the user mentions "agent ready", "isitagentready", "AI agent scan", "agent readiness", "agent-ready score", "MCP server card", "agent skills index", "markdown for agents", "content signals", "web bot auth", "agent discovery", "RFC 9727", "RFC 8288", "RFC 9728", "SEP-1649", "WebMCP", "x402", "UCP", "ACP", or wants to make a website discoverable and usable by AI agents.

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Discover and configure Bluetooth and Wi-Fi accessories using AccessorySetupKit. Use when presenting a privacy-preserving accessory picker, defining discovery descriptors for BLE or Wi-Fi devices, handling accessory session events, migrating from CoreBluetooth permission-based scanning, or setting up accessories without requiring broad Bluetooth permissions.

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Facilitates conversational discovery to create Architectural Decision Records (ADRs) for non-functional requirements using the ISO/IEC 25010:2023 quality model. Use when the user wants to document quality attributes, NFR decisions, security/performance/scalability architecture, or design systems with measurable quality criteria. This should trigger for requests such as Create ADR for Non-functional requirements; Document Non-functional requirements; Capture Non-functional requirements; Generate Non-functional requirements in an ADR. Part of cursor-rules-java project

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Nominates and assesses CRISPR off-target sites genome-wide. Enumerates candidate sites by mismatch and bulge tolerance with Cas-OFFinder/CRISPRitz, ranks them with the published CFD score (SpCas9-only, relative ranker) or MIT/CRISTA/energy models, runs variant-aware screening against gnomAD/individual genomes (CRISPRme), and frames the empirical genome-wide discovery assays (GUIDE-seq, CIRCLE-seq, CHANGE-seq, DISCOVER-seq, Digenome-seq) and high-fidelity nuclease choice (HiFi Cas9, Sniper-Cas9, eSpCas9, SpCas9-HF1). Use when assessing guide RNA specificity, choosing among candidate guides, screening a therapeutic guide against population variation, or planning empirical off-target validation. Distinguishes predicted vs detected vs validated. On-target activity scoring and deaminase (Cas-independent) base/prime-editor off-targets are separate skills.

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