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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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Performs structure-based virtual screening using AutoDock Vina, SMINA, GNINA (CNN scoring), and DiffDock-L hybrid workflows with explicit choice rules across rigid vs flexible docking, cross-docking vs self-docking, binding-site detection (P2Rank, fpocket), receptor preparation (PDB2PQR, PROPKA), ligand preparation (meeko, OpenBabel), and ultralarge-library screening (ZINC22, Enamine REAL). Use when screening chemical libraries against a protein target to find candidate binders, ranking docking poses, or selecting a docking workflow for a specific scenario.

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Performs 3D shape-based similarity searching using ROCS (OpenEye), USRCAT (ultra-fast), Open3DAlign (RDKit), ESPSim (electrostatic), and ShaEP with explicit handling of Tanimoto-Combo (shape + color), shape vs ECFP4 complementarity, conformer-ensemble searching, alignment optimization, and scaffold hopping. Use when searching for shape-mimicking compounds with different scaffolds, identifying bioisosteric replacements, prospective scaffold hopping, or expanding hit series beyond 2D similarity.

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Validates docked / generated protein-ligand poses using PoseBusters physical-validity tests, strain energy quantification, geometric checks (planarity, vdW overlap, bond/angle distortion), and pose-energy reasonableness. Filters AI-docking outputs (DiffDock, EquiBind, NeuralPLexer) where ~50% of poses fail physical-validity tests. Use when QC-ing docking results, comparing classical vs ML docking outputs, or filtering pose lists before SAR analysis.

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Analyzes CUT&RUN (Skene Henikoff 2017) and CUT&Tag (Kaya-Okur 2019) chromatin profiling data. Handles SEACR vs MACS2 peak calling (with the btaf375 2025 benchmark guidance), pA-MNase vs pA-Tn5 vs pAG-Tn5 chimera differences, E. coli spike-in carryover normalization, IgG-only control logic (no input), characteristic fragment-size signatures (25-75 bp for CUT&Tag), and lower depth requirements (5M reads typical vs 25M for ChIP). Use when calling peaks from CUT&RUN/CUT&Tag, scaling by E. coli spike-in carryover, choosing SEACR norm mode, or comparing CUT&RUN/Tag results to traditional ChIP.

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Discovers de novo motifs and tests known motif enrichment in ChIP-seq, ATAC-seq, or other peak sequences using HOMER, MEME-ChIP (STREME, CentriMo, TOMTOM, FIMO), monaLisa, and AME. Handles background selection (GC-matched, dinucleotide-shuffled, Markov order-2, peak-flanks), motif databases (JASPAR 2024 CORE PWMs, JASPAR 2026 deep-learning collection, HOCOMOCO v12, HOMER built-in), centrally-enriched motif testing, and differential motif analysis. Use when identifying TF binding motifs in peaks, testing for known TF enrichment, scanning for motif instances, comparing motif content between conditions, or interpreting motifs from deep learning models.

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Process and analyze single-cell ATAC-seq data with Signac, ArchR, SnapATAC2, or Cell Ranger ATAC. Use when handling 10X scATAC or 10X Multiome (paired RNA+ATAC) data, performing per-cell QC, choosing between ArchR/Signac/SnapATAC2 ecosystems, building per-cluster consensus peaksets, integrating with paired scRNA-seq, doublet detection (AMULET vs ArchR vs scDblFinder), or running pseudobulk differential accessibility per cluster.

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Analyzes alternative splicing from PacBio Iso-Seq (HiFi, Kinnex/MAS-Iso-seq) and Oxford Nanopore (direct cDNA, direct RNA, R10.4.1+) long-read RNA-seq with full-isoform resolution. Tools include FLAIR (correct/collapse/quantify/diffSplice for PacBio + ONT), IsoQuant (de-novo or annotation-guided isoform discovery 2024 SOTA), Bambu (annotation-aware Bayesian discovery + quantification with Novel Discovery Rate), SQANTI3/SQANTI-LR (isoform classification: FSM/ISM/NIC/NNC + artifact flags), rMATS-long (event calling on long-read isoforms), and minimap2 (-ax splice:hq for HiFi; -ax splice -k14 for ONT cDNA; add -uf only for direct RNA or stranded cDNA preps). Solves microexon detection, recursive splicing, complex multi-exon isoforms, and DTU without transcript-quantification uncertainty. Use when short-read AS limitations (anchor length, complex isoforms, microexons, recursive splicing, transcript ambiguity) demand full-isoform resolution.

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Detect transcription factor binding footprints in ATAC-seq using TOBIAS, HINT-ATAC, Wellington, or scprinter. Use when identifying bound TF sites within accessible regions, correcting Tn5 insertion bias before footprinting, choosing between cleavage-based and aggregate-based footprinters, or comparing differential TF activity between conditions.

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Call accessible chromatin regions from ATAC-seq BAM files using MACS3, MACS2, Genrich, or HMMRATAC. Use when identifying open chromatin from aligned ATAC-seq, choosing between point-source vs HMM peak callers, applying ENCODE-style pseudoreplicate IDR, removing blacklist regions, or fixing 501bp consensus peaks for downstream differential analysis.

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Use this skill when the user asks about towing + recovery operations — separate FMCSA authority class, light-duty vs medium-duty vs heavy-duty wrecker rules, AAA + AAA-Plus contracts, Roadside-Assistance (RA) operations, "non-consensual tow" rules + state-by-state, and how towing operations differ from general freight. Reference state Public Utility Commission + 49 CFR 395 application.

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Use this skill when the user asks about workers compensation for trucking — required by state law, classification of drivers, premium calculation (rate × experience modifier × payroll), Common Claim types in trucking, returning injured drivers to work, claims management, premium reduction strategies, and the difference between WC and Occupational Accident insurance for owner-operators. Reference state WC laws + IFTA / fleet insurance.

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Use this skill when the user asks about state-specific trucking taxes BEYOND IFTA — NY Highway Use Tax (HUT), KY Kentucky Intrastate Tax (KIT), Oregon Weight-Mile Tax, New Mexico Weight-Distance Tax, Connecticut Highway Use Fee, or other state-level road-use taxes for commercial vehicles. Covers thresholds, rates, registration, filing cadence, and how these differ from IFTA. Reference state DOT/DOR resources.

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Use this skill when the user asks about CMV oilfield operations — the 24-hour restart exemption (49 CFR 395.1(d)), oilfield-specific HOS rules, hot oil hauling, specialty equipment (winch trucks, kill trucks, frac sand haulers, water haulers), Texas Railroad Commission permitting, oilfield insurance specifics, and how oilfield operations differ from standard OTR trucking. Cite 49 CFR 395.1(d).

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Use this skill when the user asks about the financial differences between being an owner-operator vs company driver — gross pay, expenses, net pay, capital requirements, risk tolerance, lifestyle, and how to evaluate the path. Reference industry pay surveys.

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Use this skill to understand the 6 levels of FMCSA roadside inspections and what each covers. Helps drivers know what to expect and helps carriers respond to inspection types.

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Use this skill when the user asks about Household Goods (HHG) movers — 49 CFR 375 + 376 consumer protection rules, FMCSA HHG-specific authority, mover certification, binding vs non-binding estimates, dispute resolution, weight ticket requirements, valuation coverage, and how HHG operations differ from general freight. Cite 49 CFR 375.

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Use this skill to understand the International Registration Plan (IRP). Covers when you need to register apportioned, how it differs from IFTA, and quarterly fees.

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Use this skill when the user asks specifically about preparing for the New Entrant Safety Audit (NESA) under 49 CFR 385 Subpart D — different from a Compliance Review. Covers what auditors look at, the 18-month window, automatic failure conditions, the 60-day fix window, what to NOT do, and how to convert from "new entrant" to permanent authority. Cite 49 CFR 385.301-321.

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Use this skill when the user asks anything that touches US Department of Transportation (DOT) or Federal Motor Carrier Safety Administration (FMCSA) regulation for commercial motor vehicles (CMVs) — including who's regulated, MC vs DOT number differences, operating authority, BOC-3 process agents, MCS-150 biennial updates, intrastate vs interstate distinctions, exemptions, or pointing to the right CFR section. Cite the actual regulation when answering. Don't guess; if you're not sure which Part applies, ask the user to clarify the operation type (for-hire vs private, passenger vs property, intra vs interstate, hazmat, gross weight rating).

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Use this skill when the user asks about FMCSA investigation types — Focused Investigation vs Comprehensive Review vs Compliance Review (CR) vs Investigation, when each is triggered, scope differences, on-site vs off-site, and how to prepare for each. Cite 49 CFR 385 Subpart C + D.

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Use this skill when the user asks about CMV operation types — Dedicated, OTR (Over-the-Road), Regional, Local, and the differences in driver lifestyle, pay, equipment, home time, hours, and customer mix. Reference industry segmentation conventions.

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Use this skill when sorting paperwork between a driver's personnel file and the regulated DQ file. Covers FMCSA-required documents vs employer documents, audit-scope vs HR-scope, retention differences.

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Use this skill when the user asks the economic + operational tradeoffs of broker-mediated freight vs direct shipper relationships — margin difference, capital + operational cost, sales effort, payment terms, relationship investment, when to pursue direct, and the hybrid model. Reference industry research on freight broker margins.

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。