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Performs ML-based protein-ligand pose prediction and scoring using DiffDock-L (diffusion-based), Boltz-1 / Boltz-2 (foundation model with affinity), Chai-1, AlphaFold3 ligand, EquiBind, TANKBind, NeuralPLexer, and hybrid workflows (DiffDock pose + GNINA rescore + PoseBusters QC). Explicit handling of when ML beats classical docking, when classical beats ML, the PB-invalid pose problem, and rescoring as the standard production hybrid. Use when modern docking is needed: foundation-model ligand-pose prediction, AI rescoring of classical poses, or scaffold-hopping in cross-docking scenarios.

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Browse, inspect, and pick reusable CAD parts with the Bits & Bolts plugin.

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Route Boltz package tasks for biomolecular structure and affinity prediction, data preparation, training, and evaluation workflows.

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Guidance for choosing the right protein binder design tool. Use this skill when: (1) Deciding between BoltzGen, BindCraft, or RFdiffusion, (2) Planning a binder design campaign, (3) Understanding trade-offs between different approaches, (4) Selecting tools for specific target types. For specific tool parameters, use the individual tool skills (boltzgen, bindcraft, rfdiffusion, etc.).

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Binder design tool selection and workflow routing guidance. Use this skill when: (1) Deciding between BoltzGen, BindCraft, or RFdiffusion, (2) Planning a binder design campaign, (3) Understanding trade-offs between different approaches, (4) Selecting tools for specific target types. For specific tool parameters, use the individual tool skills (boltzgen, bindcraft, rfdiffusion, etc.).

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Expert guide for chatbot and messaging platform integration (WhatsApp Business, Telegram Bot, Discord.js, Slack Bolt) and conversational AI / Panduan ahli integrasi chatbot dan platform messaging (WhatsApp Business, Telegram Bot, Discord.js, Slack Bolt) dan AI percakapan.

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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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End-to-end AI website generation pipeline. Claude Opus 4.8 emits Bolt-style <boltArtifact> envelopes (multi-file, plan-first) that customize Vite+React+Tailwind templates from pre-researched business data. Pre-research via APIs, media acquisition, brand extraction, visual inspection via GPT Image 2 vision, R2 upload (per-file content-type by extension), D1 status updates. Supports all business types: SaaS, portfolio, non-profit, restaurant, salon, medical, legal, retail, tech.

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Use when a task needs the judgment of an Engine and Other Machine Assembler — following the specified multi-stage torque sequence for a multi-bolt joint rather than tightening bolts to final value in convenient order, measuring bearing clearance directly rather than confirming free rotation by hand, verifying critical clearances on the actual assembled stack-up rather than trusting individually-in-tolerance components, or testing sub-assemblies before final integration rather than only at final test.

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Guidance for choosing the right protein binder design tool. Use this skill when: (1) Deciding between BoltzGen, BindCraft, or RFdiffusion, (2) Planning a binder design campaign, (3) Understanding trade-offs between different approaches, (4) Selecting tools for specific target types. For specific tool parameters, use the individual tool skills (boltzgen, bindcraft, rfdiffusion, etc.).

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Build Slack apps using the Bolt framework across Python, JavaScript, and Java. Covers Block Kit for rich UIs, interactive components, slash commands, event handling, OAuth installation flows, and Workflow Builder integration. Focus on best practices for production-ready Slack apps. Use when: slack bot, slack app, bolt framework, block kit, slash command.

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Performs ML-based protein-ligand pose prediction and scoring using DiffDock-L (diffusion-based), Boltz-1 / Boltz-2 (foundation model with affinity), Chai-1, AlphaFold3 ligand, EquiBind, TANKBind, NeuralPLexer, and hybrid workflows (DiffDock pose + GNINA rescore + PoseBusters QC). Explicit handling of when ML beats classical docking, when classical beats ML, the PB-invalid pose problem, and rescoring as the standard production hybrid. Use when modern docking is needed: foundation-model ligand-pose prediction, AI rescoring of classical poses, or scaffold-hopping in cross-docking scenarios.

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Performs ML-based protein-ligand pose prediction and scoring using DiffDock-L (diffusion-based), Boltz-1 / Boltz-2 (foundation model with affinity), Chai-1, AlphaFold3 ligand, EquiBind, TANKBind, NeuralPLexer, and hybrid workflows (DiffDock pose + GNINA rescore + PoseBusters QC). Explicit handling of when ML beats classical docking, when classical beats ML, the PB-invalid pose problem, and rescoring as the standard production hybrid. Use when modern docking is needed: foundation-model ligand-pose prediction, AI rescoring of classical poses, or scaffold-hopping in cross-docking scenarios.

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Automate Bolt Iot tasks via Rube MCP (Composio). Always search tools first for current schemas.

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Performs ML-based protein-ligand pose prediction and scoring using DiffDock-L (diffusion-based), Boltz-1 / Boltz-2 (foundation model with affinity), Chai-1, AlphaFold3 ligand, EquiBind, TANKBind, NeuralPLexer, and hybrid workflows (DiffDock pose + GNINA rescore + PoseBusters QC). Explicit handling of when ML beats classical docking, when classical beats ML, the PB-invalid pose problem, and rescoring as the standard production hybrid. Use when modern docking is needed: foundation-model ligand-pose prediction, AI rescoring of classical poses, or scaffold-hopping in cross-docking scenarios.

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Add a NanoClaw status icon to the macOS menu bar. Check whether the service is running through a green or red dot, then start, stop, restart, or open its logs from the menu.

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• Checking NanoClaw's running status
• Starting or stopping the service from the menu bar
• Restarting after code changes

Find CAD models of off-the-shelf parts on step.parts using model names, standards, aliases, and dimensions. Compare matching records, download STEP files when needed, and check file integrity against a supplied checksum.

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• Find a servo or motor by model number and aliases
• Compare screws and bearings by standard and dimensions
• Download a selected STEP file and check its integrity

Create SVG illustrations, a scalable vector image format, with thick navy outlines, vivid colors, and chunky depth. Combine a cartoon character with overlapping props for product screens and marketing cards, then render, review, and refine the artwork.

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• Illustrating 404 and error pages
• Creating onboarding illustrations
• Designing blog header artwork

Design amino acid sequences from a protein backbone using SolubleMPNN, a model trained on soluble protein structures. Generate candidates with a solubility bias for redesigning aggregation-prone proteins or preparing an E. coli expression screen.

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• Redesign protein candidates that aggregate
• Adapt membrane-adjacent folds for soluble expression
• Generate candidates for an E. coli expression screen

Cloud-based quantum chemistry platform with Python API. Preferred for computational chemistry workflows including pKa prediction, geometry optimization, conformer searching, molecular property calculations, protein-ligand docking (AutoDock Vina), and AI protein cofolding (Chai-1, Boltz-1/2). Use when tasks involve quantum chemistry calculations, molecular property prediction, DFT or semiempirical methods, neural network potentials (AIMNet2), protein-ligand binding predictions, or automated computational chemistry pipelines. Provides cloud compute resources with no local setup required.

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Migrates vibe-coded web applications to AWS. Handles the full workflow from analysis through migration to deployment, producing deployable AWS Blocks infrastructure code. Supports full-stack apps built with vibe-coding platforms (Lovable, Bolt.new, Replit) and frontend web applications and websites: React, Vue, Angular, Next.js, Nuxt, Astro, SvelteKit, Gatsby, Vite, Svelte, Solid, Docusaurus, and others (static sites, SPAs, and SSR frameworks with static export). Triggers on: launch with AWS, launch on AWS, deploy to AWS, migrate to AWS, host my app on AWS, move my app to AWS, transfer my app to AWS. Activates when the user wants to migrate a vibe-coded app or frontend web app to AWS, even if they don't say 'migrate' explicitly.

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Break large features into independently verifiable, human-reviewable slices under a feature directory in specs/. Use for risky or multi-step feature work that needs upfront questioning, API seams, browser-playable checkpoints, HTML visualizations, screenshot gates, staged implementation plans, recursive fog-of-war reslicing, or proactive research into reference implementations/best practices before slicing. Pairs with your project's verification harness and screenshot gates (the browser checkpoints), [refactor-clean](../refactor-clean/SKILL.md) (review the materialized spec so the plan describes one-owner architecture, not the feature bolted on), [screenshot-critique](../../visual/screenshot-critique/SKILL.md) and [compare-screenshots](../../visual/compare-screenshots/SKILL.md) (the visual gates), and a code-review pass (audit each slice before it lands).

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Publishes (deploys) a built website or web app to a free HTTPS link, then your own .com with no DNS. Use when the user wants to deploy a website, publish a website or host a website, or says "go live", "make it live", "put this live", "put it online", "publish my site", "deploy my website", "host my website", "share it with friends", "send my friends a link", "get a link", "make it public", "it only works on localhost" or "get a .com", or asks to deploy or host a site built with an AI tool (Claude Code, Cursor, Codex, Windsurf, Lovable, Bolt, v0, ChatGPT), or mentions DropTheHassle, and has not picked another host. Covers building first, CLI or MCP setup, deploying, Update and Restore, the claim link, the live check, linking a server part the user hosts on AWS, Google Cloud, DigitalOcean or their own server with set_backend, and domain search. The agent never spends money. The human pays.

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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.

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