「pdb」の検索結果

Query UniProt REST API: search by gene/protein name, fetch FASTA, map IDs (Ensembl, PDB, RefSeq), access Swiss-Prot annotations. Use bioservices for multi-DB access; alphafold-database-access for structures.

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3Dmol.js WebGL molecular visualization emitted as self-contained HTML. Render structures (PDB/SDF/XYZ/MOL2/cube) with stick, sphere, cartoon, line, and surface styles; animate trajectories with a frame-delay (interval, ms) control; and animate vibrational normal modes via vibrate() from per-atom dx/dy/dz displacements or from precomputed frames. Output standalone HTML that loads 3Dmol from a CDN, with optional play/pause and speed controls. Use for transition-state imaginary-mode animations, MD or reaction-path playback, docking poses, and orbital/density isosurfaces. For static 2D chemical structure drawings use rdkit-chemdraw-cdxml; for 2D statistical plots use matplotlib or plotly.

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Guide CUDA-enabled BindCraft protein-binder design from target PDB preparation through AF2/MPNN/PyRosetta execution, filtering, output analysis, and conservative troubleshooting.

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Use AlphaFold 3 PyTorch for protein and biomolecular structure-prediction workflows, heterogeneous molecule inputs, PDB/mmCIF/MSA/template preparation, bounded model inference, training configuration, and local CLI or Gradio operation.

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Debug Python: pdb REPL + debugpy remote (DAP).

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WordPress plugin development with hooks, security, REST API, custom post types. Use for plugin creation, $wpdb queries, Settings API, or encountering SQL injection, XSS, CSRF, nonce errors.

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Structure similarity search with Foldseek. Use this skill when: (1) Finding similar structures in PDB/AFDB databases, (2) Structural homology search, (3) Database queries by 3D structure, (4) Finding remote homologs not detected by sequence, (5) Clustering structures by similarity. For sequence similarity, use uniprot BLAST. For structure prediction, use chai or boltz.

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Think and work like an expert Crop Protection Scientist. Use when a task calls for Crop Protection Scientist judgment. Reasons from IPM, EIL/ET, and FRAC/HRAC/IRAC MoA rotation through GEP/EPPO efficacy trials, CDMS label law, BBCH timing, DRT application, PPDB/fate modeling, and MRL/GAP alignment while treating resistance, drift, herbicide carryover, and abiotic mimicry as first-class failure modes.

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Deploy, manage, and debug Kubernetes in production — Deployments, Services, Gateway API, Service Mesh (Istio/Linkerd/Cilium), eBPF observability (Cilium Hubble), security hardening (Pod Security Standards, OPA/Kyverno, seccomp, runtime security with Falco/Tetragon), Helm, HPA, PDB, topology spread, and debugging. Use when user asks to write K8s manifests, deploy to a cluster, debug pods, set up Gateway API, configure autoscaling, or harden cluster security. Do NOT use for Dockerfiles (use docker), CI/CD pipeline design (use ci-cd), or Terraform infrastructure (use terraform).

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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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Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database.

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Access AlphaFold's 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.

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Kubernetes 工作负载编排，覆盖 Deployment / Service / Ingress / HPA / PDB。Helm Chart 管理、ArgoCD GitOps 部署、资源调优、高可用设计。

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DiffDock and DiffDock-L diffusion-based molecular docking. Use for blind protein-small-molecule pose prediction from a PDB file or sequence plus SMILES/SDF/MOL2, batch docking over a CSV of complexes, virtual screening triage, sampling multiple poses per complex, and reading the confidence score correctly. Also trigger on DiffDock, DiffDock-L, inference.py, confidence_model, samples_per_complex, ESM embedding preparation for docking, or blind docking without a defined box. Not for binding affinity prediction — the confidence score ranks pose plausibility, not potency.

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Use when a user asks to investigate, check, enrich, or characterize an IP address (IPv4 or IPv6). Chains VirusTotal, Shodan, AbuseIPDB, GreyNoise, OTX, and optionally Censys in parallel, then consolidates findings and prioritizes follow-up IOCs. Invoked by /cti-orchestrator when the target is an IP.

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Use when you need abuse-report history for an IPv4/IPv6 address — confidence score, total reports, distinct reporters, usage type. IP-only. Commonly invoked by /ip-investigation. Retrieval only.

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Use when developing GIMP 3.0+ plugins in Python 3 - procedure registration, image and layer operations, GEGL operations, PDB calls, dialogs and progress bars, file export, or batch processing plugins

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Plans, executes, and validates Google Kubernetes Engine (GKE) cluster upgrades and maintenance operations for both Standard and Autopilot clusters. Produces upgrade plans, pre/post-upgrade checklists, maintenance runbooks with gcloud commands, release channel strategy, and troubleshooting guides. Handles node pool upgrade strategies (surge, blue-green), version compatibility, PDB management, and workload-specific concerns (stateful, GPU, operators). Use this skill whenever the user mentions GKE upgrades, Kubernetes version bumps, node pool maintenance, GKE patching, cluster version management, release channel selection, maintenance windows, surge upgrades, stuck upgrades, or any GKE lifecycle management task — even casual mentions like "we need to upgrade our clusters" or "plan our next GKE maintenance" or "our upgrade is stuck." Don't use for GKE cluster creation, application onboarding, general networking/routing setup, or security policy configurations (use gke-basics or relevant GKE skills instead).

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Generate production-grade Kubernetes manifests — Deployments with probes and security contexts, Services, Ingress with TLS, HPA, PDB, NetworkPolicy, ConfigMaps, Secrets — with optional Helm charts, Kustomize overlays, Istio mesh, and ArgoCD GitOps

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MUST USE for any real runtime debugging across ANY language or binary — crashes, silent failures, wrong responses, stuck processes, memory leaks, async misbehavior, unexplained timing, reverse engineering. Runs a hypothesis-driven loop: form ≥3 hypotheses, investigate in parallel, after 2 failed rounds spawn Oracles from orthogonal angles, confirm root cause, lock with a failing test, fix minimally, QA by actually USING the system, scrub artifacts. The actual HOW lives in `references/` — READ THEM. Triggers: 'debug this', 'why is X not working', 'hanging', 'attach a debugger', 'reverse engineer', 'pwndbg', 'gdb', 'lldb', 'node inspect', 'tsx debug', 'pdb', 'dlv', 'delve', 'rust-gdb', 'set a breakpoint', 'context window exploded', 'why is the response empty', 'attach the debugger', 'debug it', 'why is this happening', 'trace this bug', 'reproduce and fix', 'silent failure', 'HTTP 200 but empty', 'why did it stop', 'inspect the binary', 'reverse engineering', 'playwright'.

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Access AlphaFold's 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.

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。

Debug Python: pdb REPL + debugpy remote (DAP).

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。

Make a WooCommerce plugin HPOS-compatible (High-Performance Order Storage, default-on in WC 10.x) — declare via FeaturesUtil::declare_compatibility on before_woocommerce_init, replace $wpdb->postmeta / WP_Query order code with wc_get_orders + WC_Order::get_meta / update_meta_data, gate runtime branches on OrderUtil::custom_orders_table_usage_is_enabled, build admin hook names dynamically with OrderUtil::get_order_admin_screen (HPOS = woocommerce_page_wc-orders, legacy = shop_order). Use when scaffolding an order-touching plugin, auditing existing code for HPOS readiness, or fixing post-WC-10 silent breakage. Triggers on shop_order, get_post_meta with order context, FeaturesUtil, OrderUtil, custom_order_tables, before_woocommerce_init.

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Debug Python: pdb REPL + debugpy remote (DAP).

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。