atomcad
Interact with atomCAD node networks programmatically. Query, edit, and replace CAD geometry nodes for atomic/molecular structure design. Use when working with atomCAD projects or when the user wants to manipulate node networks, create CSG shapes, or design atomic structures.
chembl-database
Query ChEMBL's bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.
safe-calculator
A safe calculator for mathematical expressions
studio-assistant-performer-guide
Lists the exact current Studio Assistant mutation surface for Tal, Dance, Performer, Act, participant, relation, and install/import actions. Use when the assistant must produce, inspect, or verify an assistant-actions block or reason about allowed fields.
cirq
Quantum computing framework for building, simulating, optimizing, and executing quantum circuits. Use this skill when working with quantum algorithms, quantum circuit design, quantum simulation (noiseless or noisy), running on quantum hardware (Google, IonQ, AQT, Pasqal), circuit optimization and compilation, noise modeling and characterization, or quantum experiments and benchmarking (VQE, QAOA, QPE, randomized benchmarking).
adaptyv
Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting experiments via API, tracking experiment status, downloading results, optimizing protein sequences for better expression using computational tools (NetSolP, SoluProt, SolubleMPNN, ESM), or managing protein design workflows with wet-lab validation.
biomni
Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis. Use this skill when conducting multi-step biomedical research including CRISPR screening design, single-cell RNA-seq analysis, ADMET prediction, GWAS interpretation, rare disease diagnosis, or lab protocol optimization. Leverages LLM reasoning with code execution and integrated biomedical databases.
mfe-reality
Physical applications of mathematics. Constants, quantum mechanics, measurement — where abstract meets embodied.
agency-evidence-collector
Screenshot-obsessed, fantasy-allergic QA specialist - Default to finding 3-5 issues, requires visual proof for everything
agency-evidence-collector
Screenshot-obsessed, fantasy-allergic QA specialist - Default to finding 3-5 issues, requires visual proof for everything
pie-dimensional-analysis
Mathematical verification for physical calculations: unit tracking algebra (exponent maps), PhysicalQuantity pattern for compound units, SI/Imperial mixed-unit handling, Buckingham pi theorem for dimensionless groups, and common engineering dimensionless numbers. Activates for unit verification, dimensional consistency checks, scaling analysis, and calculation validation across all infrastructure domains.
agency-evidence-collector
Screenshot-obsessed, fantasy-allergic QA specialist - Default to finding 3-5 issues, requires visual proof for everything
aminet-scanner
Multi-layer virus scanning for Aminet packages. Signature-based detection, heuristic hunk analysis, boot block scanning, quarantine management, and scan orchestration. Use when scanning packages, checking virus status, or managing quarantine.
spec-driven-task-decomposer
Use this skill when approved requirements and design need to be decomposed into tasks.md for Phase 3 of a Spec-Driven change. It creates atomic, traceable implementation and testing tasks, validates the plan, and should not be used to design architecture or write implementation code.
cleanup-quarantine-manager
Classify cleanup candidates and apply conservative quarantine moves with reversible manifests.
qutip
Quantum physics simulation library for open quantum systems. Use when studying master equations, Lindblad dynamics, decoherence, quantum optics, or cavity QED. Best for physics research, open system dynamics, and educational simulations. NOT for circuit-based quantum computing—use qiskit, cirq, or pennylane for quantum algorithms and hardware execution.
molecular-dynamics
Autonomous molecular dynamics simulation pipeline inspired by DynaMate (2026). Designs, executes, and analyzes complete MD workflows for protein and protein-ligand systems. Covers structure retrieval, system preparation, minimization, equilibration, production, and trajectory analysis (RMSD, RMSF, hydrogen bonds, binding free energy). Uses OpenMM as the primary engine with AmberTools for preparation. Self-correcting — detects and fixes common simulation failures. Use when users ask for MD simulations, protein stability analysis, binding free energy calculations, or "跑个分子动力学模拟". Requires OpenMM and optionally AmberTools.
qiskit
IBM quantum computing framework. Use when targeting IBM Quantum hardware, working with Qiskit Runtime for production workloads, or needing IBM optimization tools. Best for IBM hardware execution, quantum error mitigation, and enterprise quantum computing. For Google hardware use cirq; for gradient-based quantum ML use pennylane; for open quantum system simulations use qutip.
cirq
Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best for Google hardware, noise modeling, and low-level circuit design. For IBM hardware use qiskit; for quantum ML with autodiff use pennylane; for physics simulations use qutip.
pxdesign
De novo protein binder design using PXDesign. Use this skill when designing non-antibody protein binders against a target structure. Covers YAML config creation, CLI invocation, output parsing, and result interpretation. For antibody/nanobody binders, use proteus-ab instead. For structure prediction only, use proteus-fold. For scoring and screening, use proteus-scoring and proteus-screening.
boltzgen
Antibody and nanobody binder design using Proteus-AB (BoltzGen diffusion + Protenix refolding). Covers entity YAML specification, CLI invocation, protocol selection (nanobody-anything / antibody-anything), MSA modes, and output parsing. Use this skill whenever the user needs to design an antibody or nanobody binder against a protein target.
pxdesign
De novo protein binder design using PXDesign. Use this skill when designing non-antibody protein binders against a target structure. Covers YAML config creation, CLI invocation, output parsing, and result interpretation. For antibody/nanobody binders, use boltzgen instead. For structure prediction only, use proteus-fold. For scoring and screening, use by-scoring and by-screening.