'binding' 검색 결과

Trains and applies base-resolution deep learning models on ChIP-seq / ChIP-nexus / CUT&RUN data. Uses BPNet (Avsec 2021 Nat Genet 53:354; soft motif syntax from ChIP-nexus), chromBPNet (Pampari A et al 2025 Nat Genet; bias-factorized base-resolution profiles), EnFormer (Avsec 2021 Nat Methods 18:1196; 196 kb input, ~100 kb effective receptive field), DeepSEA (Zhou 2015; multi-task CNN), and JASPAR 2026 deep-learning collection (1259 BPNet ChIP models). Performs in silico mutagenesis for variant-effect prediction, DeepLIFT/Grad attribution, and TF-MoDISco motif discovery from attribution scores. Use when predicting variant effects on TF binding, discovering soft motif syntax / cooperativity, integrating ChIP-seq with sequence-only predictions, or applying precomputed JASPAR Deep Learning models to new variants.

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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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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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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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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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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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Send and receive transactional emails with Cloudflare Email Service (Email Sending + Email Routing). Use when building email sending (Workers binding or REST API), email routing, Agents SDK email handling, or integrating email into any app — Workers, Node.js, Python, Go, etc. Also use for email deliverability, SPF/DKIM/DMARC, wrangler email setup, MCP email tools, or when a coding agent needs to send emails. Even for simple requests like "add email to my Worker" — this skill has critical config details.

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Use when wrangler deploys silently fail or produce wrong artifacts, secrets upload as empty strings, custom domain DNS is not resolving, route assignment broke after rename, observability/tail logs are needed, D1/KV/R2 bindings are missing, OAuth scope errors block a command, cookies on a redirect are not attaching, or the worker exceeds CPU time. Triggers: "Tenant or user not found", "Authentication error" on wrangler d1 push, secret length is 0 after upload, route returns origin not worker, "compatibility_date too old", 1101 errors, custom_domain assignment lost on script rename. NOT for AWS Lambda / Vercel Edge / Deno Deploy (different runtimes), Cloudflare Zero Trust, or R2-specific tuning.

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Verify every visual-evidence artifact (screenshot/GIF/recording) attached to a PR carries a provenance manifest binding it to real daemon-backed truth — daemon port, run id, transcript head hash, agent node id, commit, and an honest real/fixture/mock source label — and that operator-control-panel PRs cover the required set of proof states. Use when gating a PR's proof artifacts before merge, auditing whether a "LIVE" visual claim is backed by a real daemon run versus a reused or fixture-backed mock, or defining the required state-coverage set for a control-panel change. NOT for the capture technique itself — headless Playwright, `screencapture -x -l`, non-interruptive capture (use port-daddy-agent-skill's visual-evidence doctrine), designing the receipt body schema an artifact attaches to (use agent-work-receipt-designer), or the broader dogfood/Potemkin product-quality bar (use multi-agent-authoring-product-bar).

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No-loss protocol for changing an existing mandate's output contract. Use when changing what an agent or mandate emits or how it is typed: binding a kind, declaring output_kind, kind-backfill batches, provision reconciliation, or any make-this-contract-honest sweep. NOT for creating a new agent (use create-agent).

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The Shape System — the content_ir kind registry for structured content. Use when adding, activating, or rendering a kind/shape, writing `__kind` JSON, kind schemas or samples, XML-tag/fence detection surfaces, kind components, workflow node input_kind/output_kind, or binding agent output to a kind.

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The Matrx user settings system (SettingsShell, useSetting, tab registry). Use when adding a preference or settings tab, binding a Redux slice to settings, wiring a settings deep link, or touching features/settings, components/official/settings, or components/user-preferences.

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Expert guidance for developing cross-platform desktop applications with Avalonia UI framework. Use when building, debugging, or optimizing Avalonia apps including MVVM architecture, XAML design, data binding, styling, theming, custom controls, and cross-platform deployment for Windows, macOS, Linux, iOS, Android, and WebAssembly.

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Guide for Private and Internal member testing strategies. Use when you need to test private or internal members, configure InternalsVisibleTo, or evaluate testability design. Covers design-first thinking, reflection testing, strategy pattern refactoring, AbstractLogger pattern, and decision frameworks. Keywords: private method testing, internal testing, InternalsVisibleTo, reflection testing, GetMethod BindingFlags, Meziantou.MSBuild.InternalsVisibleTo, testability design, strategy pattern refactoring, testability

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Builds full TUI apps. Terminal.Gui v2 -- views, layout (Pos/Dim), menus, dialogs, bindings, themes.

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Detect WMI event subscription persistence by analyzing Sysmon Event IDs 19, 20, and 21 for malicious EventFilter, EventConsumer, and FilterToConsumerBinding creation.

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Discover and exploit mass assignment vulnerabilities in REST APIs to escalate privileges, modify restricted fields, and bypass authorization controls by injecting unexpected parameters in API requests.

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Auditing Google Cloud Platform IAM permissions to identify overly permissive bindings, primitive role usage, service account key proliferation, and cross-project access risks using gcloud CLI, Policy Analyzer, and IAM Recommender.

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Auditing Kubernetes cluster RBAC configurations to identify overly permissive roles, wildcard permissions, dangerous ClusterRoleBindings, service account abuse, and privilege escalation paths using kubectl, rbac-tool, KubiScan, and Kubeaudit.

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Hunting skill for ssrf vulnerabilities. Built from 15 public bug bounty reports including AWS metadata SSRF (HackerOne $25k Analytics PDF, Shopify Exchange $25k, Capital One 106M-record breach, Dropbox/HelloSign $4,913), GCP metadata SSRF (Snapchat $4k), Azure IMDS SSRF (Azure DevOps $15k chain, ChatGPT Custom Actions MSRC), DNS rebinding SSRF (Concrete CMS, GitLab UrlBlocker), gopher-protocol-to-Redis-RCE (Yahoo Mail $15k), link-preview SSRF (Reddit Matrix $6k), and headless-browser PDF-generator SSRF chains. Use when hunting SSRF on any target — OOB Collaborator confirmation mandatory for blind cases.

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Server-Side Request Forgery testing checklist: SSRF discovery, blind SSRF with out-of-band, cloud metadata endpoints (AWS/GCP/Azure), SSRF filter bypass techniques (IP encoding, DNS rebinding, redirect chains), and SSRF to RCE escalation. Use for web app SSRF testing and bug bounty.

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Kubernetes cluster attack techniques covering the full attack lifecycle from initial foothold in a pod to cluster-wide compromise. Covers service account token theft and impersonation, RBAC misconfiguration exploitation including wildcard permissions and privilege escalation via role binding, direct etcd access for secret extraction, kubelet API abuse on port 10250 and read-only port 10255, pod escape via hostPID hostNetwork and hostPath volume mounts, Kubernetes secrets enumeration and decoding, admission controller bypass techniques, network policy bypass and lateral movement, cloud metadata service access from pods for credential theft on AWS EKS GCP GKE and Azure AKS, CRD and operator abuse for persistence, and node compromise via DaemonSet deployment. Tools include kubectl, kube-hunter, peirates, kubeaudit, kdigger, kubeletctl. Maps to MITRE ATT&CK T1609 Container Administration Command, T1610 Deploy Container, T1613 Container and Resource Discovery. Use this skill when assessing Kubernetes clusters,...

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