「binding」の検索結果

Performs alchemical free-energy calculations including relative binding free energy (RBFE / FEP+) and absolute binding free energy (ABFE) via OpenFE, FEP+, GROMACS, AMBER pmemd, and OpenMM with explicit lambda scheduling, soft-core potentials, MBAR/BAR analysis, cycle-closure validation, and protocol-appropriate enhanced sampling. Compares ML alternatives (Boltz-2 affinity, DeepDock). Use when ranking analogs by binding affinity beyond docking accuracy, performing prospective lead optimization, or validating SAR predictions.

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。

Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL + bias-corrected testing), BaalChIP (Bayesian beta-binomial with copy-number-aware overdispersion), and AlleleSeq (personalized diploid genome). Handles imprinted-locus awareness, X-inactivation artifacts, cancer copy-number imbalance, and integration with downstream caQTL / bQTL mapping. Use when identifying variants with allelic effects on TF binding, fine-mapping causal regulatory variants, validating deep-learning variant predictions, or characterizing cis-acting regulatory effects.

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。

Query BindingDB for measured drug-target binding affinities (Ki, Kd, IC50, EC50). Search by target (UniProt ID), compound (SMILES/name), or pathogen. Essential for drug discovery, lead optimization, polypharmacology analysis, and structure-activity relationship (SAR) studies.

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。

Harden LDAP directory services against common attacks including credential harvesting, LDAP injection, anonymous binding, and channel binding bypass. Covers LDAPS enforcement, channel binding, LDAP si

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。

Harden LDAP directory services against common attacks including credential harvesting, LDAP injection, anonymous binding, and channel binding bypass. Covers LDAPS enforcement, channel binding, LDAP si

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。

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

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。

Performs alchemical free-energy calculations including relative binding free energy (RBFE / FEP+) and absolute binding free energy (ABFE) via OpenFE, FEP+, GROMACS, AMBER pmemd, and OpenMM with explicit lambda window scheduling, soft-core potentials, REST2 enhanced sampling, MBAR/BAR analysis, and cycle closure validation. Compares ML alternatives (Boltz-2 affinity, DeepDock). Use when ranking analogs by binding affinity beyond docking accuracy, performing prospective lead optimization, or validating SAR predictions.

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。

Infer or annotate TCR antigen specificity by unsupervised clustering (TCRdist/tcrdist3, GLIPH2, clusTCR, GIANA) and database lookup (VDJdb, IEDB, McPAS-TCR), and rank candidates with supervised predictors (ERGO-II, NetTCR-2.x, pMTnet) under explicit caveats. Encodes the central truth that general TCR-epitope prediction for UNSEEN epitopes essentially does not work (collapses to near-random; IMMREP22, Grazioli 2022) because labeled data is dominated by a few immunodominant epitopes and there is no true negative set — so clustering for discovery is the honest task and de-novo binding needs wet-lab validation. Use when annotating TCR specificity or grouping a repertoire. Epitope/MHC context lives in mhc-binding-prediction.

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。

Identify tumor neoantigens from somatic variants with pVACtools (pVACseq/pVACfuse/pVACbind/pVACvector/pVACview) for personalized cancer vaccines and checkpoint biomarkers. Encodes the field's hard truth that binding prediction is the easy, near-solved part and single-digit-percent PPV lives downstream — so it centers clonality/CCF, HLA LOH (the silent invalidator), expression, proximal-variant phasing, agretopicity/foreignness quality, and the predicted->presented->immunogenic validation tiers. Use when nominating vaccine targets, ranking neoantigens, or building a tumor-to-candidate pipeline. Binding details in mhc-binding-prediction; ranking in immunogenicity-scoring.

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。

Predict peptide-MHC class II (HLA-DR/DQ/DP) binding and presentation for CD4 T-cell epitopes with NetMHCIIpan-4.3 and MixMHC2pred-2.0. Covers why class II is far less reliable than class I (open binding groove, 9-mer register ambiguity, sparse noisy training data, DR>DP>DQ accuracy asymmetry), the DQ/DP heterodimer alpha/beta pairing trap, and the looser 1%/5% %Rank thresholds. Use when predicting CD4 epitopes for vaccine help, mapping class II neoantigens, or scoring long peptides against DR/DQ/DP. For CD8/class I see mhc-binding-prediction.

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。

Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL + bias-corrected testing), BaalChIP (Bayesian beta-binomial with copy-number-aware overdispersion), and AlleleSeq (personalized diploid genome). Handles imprinted-locus awareness, X-inactivation artifacts, cancer copy-number imbalance, and integration with downstream caQTL / bQTL mapping. Use when identifying variants with allelic effects on TF binding, fine-mapping causal regulatory variants, validating deep-learning variant predictions, or characterizing cis-acting regulatory effects.

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。

Performs alchemical free-energy calculations including relative binding free energy (RBFE / FEP+) and absolute binding free energy (ABFE) via OpenFE, FEP+, GROMACS, AMBER pmemd, and OpenMM with explicit lambda window scheduling, soft-core potentials, REST2 enhanced sampling, MBAR/BAR analysis, and cycle closure validation. Compares ML alternatives (Boltz-2 affinity, DeepDock). Use when ranking analogs by binding affinity beyond docking accuracy, performing prospective lead optimization, or validating SAR predictions.

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。

Infer or annotate TCR antigen specificity by unsupervised clustering (TCRdist/tcrdist3, GLIPH2, clusTCR, GIANA) and database lookup (VDJdb, IEDB, McPAS-TCR), and rank candidates with supervised predictors (ERGO-II, NetTCR-2.x, pMTnet) under explicit caveats. Encodes the central truth that general TCR-epitope prediction for UNSEEN epitopes essentially does not work (collapses to near-random; IMMREP22, Grazioli 2022) because labeled data is dominated by a few immunodominant epitopes and there is no true negative set — so clustering for discovery is the honest task and de-novo binding needs wet-lab validation. Use when annotating TCR specificity or grouping a repertoire. Epitope/MHC context lives in mhc-binding-prediction.

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。

Identify tumor neoantigens from somatic variants with pVACtools (pVACseq/pVACfuse/pVACbind/pVACvector/pVACview) for personalized cancer vaccines and checkpoint biomarkers. Encodes the field's hard truth that binding prediction is the easy, near-solved part and single-digit-percent PPV lives downstream — so it centers clonality/CCF, HLA LOH (the silent invalidator), expression, proximal-variant phasing, agretopicity/foreignness quality, and the predicted->presented->immunogenic validation tiers. Use when nominating vaccine targets, ranking neoantigens, or building a tumor-to-candidate pipeline. Binding details in mhc-binding-prediction; ranking in immunogenicity-scoring.

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。

Predict peptide-MHC class II (HLA-DR/DQ/DP) binding and presentation for CD4 T-cell epitopes with NetMHCIIpan-4.3 and MixMHC2pred-2.0. Covers why class II is far less reliable than class I (open binding groove, 9-mer register ambiguity, sparse noisy training data, DR>DP>DQ accuracy asymmetry), the DQ/DP heterodimer alpha/beta pairing trap, and the looser 1%/5% %Rank thresholds. Use when predicting CD4 epitopes for vaccine help, mapping class II neoantigens, or scoring long peptides against DR/DQ/DP. For CD8/class I see mhc-binding-prediction.

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。

Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL + bias-corrected testing), BaalChIP (Bayesian beta-binomial with copy-number-aware overdispersion), and AlleleSeq (personalized diploid genome). Handles imprinted-locus awareness, X-inactivation artifacts, cancer copy-number imbalance, and integration with downstream caQTL / bQTL mapping. Use when identifying variants with allelic effects on TF binding, fine-mapping causal regulatory variants, validating deep-learning variant predictions, or characterizing cis-acting regulatory effects.

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。

Performs alchemical free-energy calculations including relative binding free energy (RBFE / FEP+) and absolute binding free energy (ABFE) via OpenFE, FEP+, GROMACS, AMBER pmemd, and OpenMM with explicit lambda window scheduling, soft-core potentials, REST2 enhanced sampling, MBAR/BAR analysis, and cycle closure validation. Compares ML alternatives (Boltz-2 affinity, DeepDock). Use when ranking analogs by binding affinity beyond docking accuracy, performing prospective lead optimization, or validating SAR predictions.

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。

Harden LDAP directory services against common attacks including credential harvesting, LDAP injection, anonymous binding, and channel binding bypass. Covers LDAPS enforcement, channel binding, LDAP si

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。

Predicts protein-small-molecule binding poses with DiffDock and DiffDock-L from PDB or sequence plus SMILES/SDF/MOL2. Covers batch docking, pose triage, confidence interpretation, and validation. Use for molecular docking and virtual-screening pose generation, not binding-affinity prediction.

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。

Internal downstream skill for ctf-sandbox-orchestrator. CTF-sandbox workflow for Kubernetes API analysis, service-account trust, RBAC edges, admission and controller behavior, cluster secrets, workload mutation, and namespace-scoped drift. Use when the user asks to inspect kube API permissions, service-account tokens, RoleBinding or ClusterRoleBinding edges, admission webhooks, controller-created pods, secret exposure, or why live workloads differ from manifests. Use only after `$ctf-sandbox-orchestrator` has already established sandbox assumptions and routed here.

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。

Finds over-permissive RBAC roles and service-account token abuse paths in a Kubernetes cluster using kubectl auth can-i, rbac-police, kubectl-who-can, and rakkess, tracing which subjects can escalate toward cluster-admin. Use when reviewing who can escalate privileges in a cluster, hunting exploitable RoleBindings during an authorized review, or validating least privilege after an RBAC change. Keywords: RBAC, ClusterRoleBinding, service account token, auth can-i, rbac-police, escalate, bind, impersonate. Do not use for designing and applying hardened RBAC - use implementing-rbac-hardening-for-kubernetes.

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。

Build or update a professional-grade design system in Figma from a codebase. Use when the user wants to create variables/tokens, build component libraries, create individual components with proper variant sets and variable bindings, set up theming (light/dark modes), document foundations, or reconcile gaps between code and Figma. Also use when the user asks to create or generate any component in Figma — even a single one — since components require proper variable foundations, variant states, and design token bindings to be production-quality. This skill teaches WHAT to build and in WHAT ORDER — it complements the `figma-use` skill which teaches HOW to call the Plugin API. Both skills should be loaded together.

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。

Build or update a professional-grade design system in Figma from a codebase. Use when the user wants to create variables/tokens, build component libraries, create individual components with proper variant sets and variable bindings, set up theming (light/dark modes), document foundations, or reconcile gaps between code and Figma. Also use when the user asks to create or generate any component in Figma — even a single one — since components require proper variable foundations, variant states, and design token bindings to be production-quality. This skill teaches WHAT to build and in WHAT ORDER — it complements the `figma-use` skill which teaches HOW to call the Plugin API. Both skills should be loaded together.

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。

Guide for implementing Shell-based navigation in .NET MAUI apps. Covers AppShell setup, visual hierarchy (FlyoutItem, TabBar, Tab, ShellContent), URI-based navigation with GoToAsync, route registration, query parameters, back navigation, flyout and tab configuration, navigation events, and navigation guards. Use when: setting up Shell navigation, adding tabs or flyout menus, navigating between pages with GoToAsync, passing parameters between pages, registering routes, customizing back button behavior, or guarding navigation with confirmation dialogs. Do not use for: deep linking from external URLs (see .NET MAUI deep linking documentation), data binding on pages (use maui-data-binding), dependency injection setup (use maui-dependency-injection), or NavigationPage-only apps that don't use Shell.

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。