「binding」の検索結果

Cofold protein-ligand, protein-protein, and nucleic-acid complexes with Boltz-2, and predict binding affinity with its trained affinity head. Use this skill to build Boltz input YAML, run structure prediction with MSAs, pocket constraints, templates, and modified residues, screen compound libraries by cofolding, and interpret confidence scores (pLDDT, pTM, ipTM, PDE) and affinity output (binder probability and log10 IC50). Also trigger on Boltz, Boltz-1, Boltz-2, cofolding, boltz predict, affinity_pred_value, affinity_probability_binary, ipTM, or open-weights AlphaFold3 alternatives.

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Turn a set of structures into absorption, distribution, metabolism, excretion, and toxicity estimates with ADMET-AI, and read them as a developability verdict rather than a table of numbers. Use this skill to run batch prediction over a library, interpret each endpoint against its DrugBank-approved percentile, and flag the liabilities that stop a series — hERG blockade, CYP inhibition, poor Caco-2 permeability, high clearance, and plasma protein binding. Also trigger on ADMET-AI, admet_ai, Chemprop-RDKit, hERG liability, CYP3A4 inhibition, Caco-2, bioavailability prediction, or developability triage.

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How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval. Use this skill whenever the user mentions Adaptyv, Foundry API, protein binding assays, protein screening experiments, BLI/SPR assays, thermostability assays, or wants to submit protein sequences for experimental characterization. Also trigger when code imports `adaptyv`, `adaptyv_sdk`, or `FoundryClient`, or references `foundry-api-public.adaptyvbio.com`.

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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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Compute relative and absolute binding free energies with the Open Free Energy toolkit — the rigorous alchemical alternative to docking scores when a congeneric series needs reliable potency ranking. Use this skill to plan a perturbation network over a ligand set, choose atom mappings, run hybrid-topology or separated-topology protocols, and analyse the result — per-edge ΔΔG with uncertainty, cycle-closure error, and mean unsigned error against measured affinities. Also trigger on OpenFE, alchemical transformation, thermodynamic cycle, RBFE, ABFE, SepTop, lambda window, MBAR, cycle closure, or perturbation map.

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Retrieve protein sequences, annotation, and structures from UniProtKB, the RCSB PDB, and AlphaFold DB. Use this skill to resolve a gene or protein name to a UniProt accession, pull sequences and FASTA files, find binding sites and domains, search the PDB by UniProt accession, sequence, ligand, or text, download mmCIF/PDB coordinates and biological assemblies, fetch AlphaFold models with their pLDDT confidence, and check whether a structure is actually usable before docking or simulating it. Also trigger on UniProt accessions, PDB ids, rest.uniprot.org, search.rcsb.org, files.rcsb.org, alphafold.ebi.ac.uk, id mapping, SEQRES, or missing residues.

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Access a collection of open-source molecular design and structural biology tools on the Tamarind Bio platform, via its REST API or MCP server — no local GPUs required. Tamarind bundles popular open-source models for structure prediction (AlphaFold, Boltz, Chai, ESMFold), protein, binder, and de novo design (RFdiffusion, ProteinMPNN, BoltzGen), antibody and nanobody design and developability, protein-ligand docking (DiffDock, Autodock Vina), binding-affinity prediction, MSA generation, and molecular dynamics. Use when the user mentions Tamarind or tamarind.bio, wants to run any of these open-source tools in the cloud, references app.tamarind.bio/api or the x-api-key header, or needs to submit batches of sequences for structural or biophysical characterization.

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Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein and protein-ligand systems with PDBFixer, choose force fields and water models (AMBER14, CHARMM36m, ff19SB, GAFF2, TIP3P), solvate and add ions, run energy minimization, NVT/NPT equilibration and production MD on GPU, then analyze trajectories for RMSD, RMSF, radius of gyration, hydrogen bonds, native contacts, PCA and free energy surfaces. Use this skill for protein stability under mutation, ligand binding-mode and residence-time questions, conformational sampling, membrane proteins, and disordered ensembles. Also trigger on OpenMM, MDAnalysis, mdtraj, Simulation.step, LangevinMiddleIntegrator, PDBFixer, DCD or XTC trajectory, RMSD analysis, or production MD.

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Use when explaining System V AMD64, ARM AAPCS, RISC-V psABI, stack frames, variadic calls, or FFI register rules. Not for the Rust FFI binding layer: use rust-ffi.

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ASP.NET Core web framework conventions: Minimal API vs MVC controllers, Program.cs composition, DI lifetimes (Scoped/Singleton/Transient), Options pattern with IOptions<T>, middleware ordering (HTTPS redirect → routing → authentication → authorization), model binding and validation (FluentValidation / DataAnnotations), ProblemDetails error handling, structured logging with ILogger<T>, configuration layering (appsettings.json + environment variables + User Secrets), and health checks. Works alongside csharp-foundation:csharp-conventions and aspnet-core-plugin:efcore-patterns. Use this skill to: - Compose Program.cs correctly — register services, configure middleware in the right order, map endpoints. - Apply the Options pattern to avoid passing raw IConfiguration into services. - Write Minimal API endpoint groups with typed results and authorization. - Handle cross-cutting errors uniformly with ProblemDetails. - Configure structured logging and health checks for production readiness. Do NOT use this skill for: - EF Core entity configuration and migrations — see aspnet-core-plugin:efcore-patterns. - C# language idioms — see csharp-foundation:csharp-conventions. - Testing — see csharp-foundation:dotnet-testing.

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Write idiomatic application code with the ClickHouse Node.js client (`@clickhouse/client`). Use this skill whenever a user is *building* against the Node.js client - configuring the client, pinging, inserting rows in JSON or raw formats, selecting and parsing results, binding query parameters, managing sessions and temporary tables, working with data types or customizing JSON parsing. Do NOT use for browser/Web client code.

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Use when designing or building any terminal user interface — choosing a layout paradigm, keybindings/interaction model, color system, data visualization, or motion. Framework-agnostic universal patterns that work with Ratatui, Ink, Textual, Bubbletea, or any TUI toolkit. For the repo's own pythinker-code TUI, use write-tui instead.

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Bootstrap new 33GOD ecosystem agents with standardized configuration. Use when creating new agents, spawning workers, deploying Yi nodes, or when the user says "spin up an agent", "create a new agent", "deploy a new worker", or needs a new agent for a specific pipeline role. Handles workspace creation, config injection, skill installation, provider mirroring, channel binding, and 33GOD ecosystem onboarding (GOD Docs, Plane, Bloodbank, memory).

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Guide for creating VS Code extensions and plugins from scratch through Marketplace publication. Use when developing a VS Code extension/plugin, adding commands or keybindings, building TreeView or Webview UI, publishing to Marketplace, or troubleshooting activation and packaging issues.

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Detects version drift between machine-readable law YAML files and the binding geldende wettekst on wetten.overheid.nl at the YAML's claimed valid_from. Catches the silent failure where authored content lags behind ingevoerde wijzigingen — a YAML dated 2025-01-01 still carrying pre-Stb.-X text. Activate as Step 0 of every regelrecht-stelselanalyse micro-cycle, before any YAML edit. Strict by design: no bypass, no normalization beyond whitespace within a single paragraph; the geldende wettekst is leading and is mirrored verbatim, including errata. Use proactively when starting a stelselanalyse cycle, before harvest/migrate/extend, or when user mentions "drift", "versie", "geldende tekst", or worries that a YAML may be stale relative to wetten.overheid.nl.

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Use before playing, blending, or retargeting GLB animation clips in PlayCanvas, or when diagnosing T-pose, frozen playback, or binding failures.

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OAuth and OIDC misconfiguration testing playbook. Use when reviewing redirect URI handling, state and nonce validation, PKCE, token audience, callback binding, and identity-provider trust flaws.

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Exploit misconfigured Kubernetes Role-Based Access Control (RBAC) to escalate privileges within a cluster. This skill covers identifying overly permissive roles and bindings, and leveraging them to gain cluster-admin access or compromise the host nodes.

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JWT and OAuth token attack playbook. Use when validating token trust, signing algorithms, key handling, claim abuse, bearer flows, and OAuth account-binding weaknesses.

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Hunts for malicious WMI permanent event subscription persistence by correlating __EventFilter, CommandLineEventConsumer/ActiveScriptEventConsumer, and FilterToConsumerBinding records from Sysmon Event IDs 19/20/21 or WMI repository exports. Activates for requests to hunt WMI persistence, detect event consumer backdoors, or analyze WMI subscription telemetry.

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UniTask async/await patterns for Unity including cancellation, lifecycle binding, and coroutine interop.

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Unity 6 UI development guide. Use when building user interfaces, menus, HUD, buttons, or any UI elements. Covers UI Toolkit (recommended for new projects — USS, UXML, UI Builder, data binding), uGUI/Canvas (legacy runtime UI), and IMGUI. Based on Unity 6.3 LTS documentation.

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Unity New Input System correctness patterns. Catches common mistakes with action reading (triggered vs IsPressed vs WasPressedThisFrame), action map switching, rebinding persistence, InputValue lifetime, PassThrough vs Value, local multiplayer device assignment, and control scheme auto-switching. PATTERN format: WHEN/WRONG/RIGHT/GOTCHA. Based on Unity 6.3 LTS.

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Use when a task needs the judgment of a Biochemist — determining enzyme kinetics (Km/Vmax, inhibition mechanism) from rate data, choosing a structural-biology method (X-ray crystallography, cryo-EM, or NMR) for a target, designing or interpreting a binding assay (ITC, SPR, fluorescence polarization), or selecting a protein-purification strategy and diagnosing why a prep failed.

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