Data Science & ML Agent Skills

Foldseek Structure Search

Performs fast and sensitive 3D protein structure similarity searches across global databases like PDB and AlphaFold DB.

RCSB PDB Structure Manager

Fetches, analyzes, and prepares protein structures from the RCSB Protein Data Bank for computational biology workflows.

UniProt Protein Database Access

Retrieves comprehensive protein sequences, functional annotations, and structural cross-references directly from the UniProt database.

Protein Design Setup

Configures and troubleshoots the environment for running serverless protein design tools via Modal and biomodals.

Protein Design Campaign Manager

Orchestrates complex protein binder design campaigns from high-level goal definition to high-throughput pipeline execution.

Protein Design Quality Control

Evaluates and filters protein designs using research-backed metrics for binding, expression, and structural integrity.

Ligand-Aware Protein Design

Designs optimized protein sequences for binding sites and enzymes using Ligand-aware Message Passing Neural Networks.

Cell-Free Protein Expression Guide

Optimizes cell-free protein synthesis (CFPS) experiments through system selection, codon optimization, and troubleshooting guidance.

Protein Binding Characterization

Provides expert guidance for Surface Plasmon Resonance (SPR) and Biolayer Interferometry (BLI) experimental design and troubleshooting.

Boltz Structure Prediction

Predicts biomolecular structures and protein-ligand complexes using the open-source Boltz-1 and Boltz-2 models.

Calibrated Explanations Plugin Auditor

Audits Calibrated Explanations (CE) plugin implementations for compliance with metadata standards, ADR contracts, and mathematical protocols.

CE Plugin Auditor

Audits Calibrated Explanations (CE) plugin implementations to ensure compliance with registry trust rules, metadata standards, and ADR requirements.

CE Pipeline Builder

Builds standardized machine learning pipelines that integrate calibrated explanations for model interpretability and reliability.

Chai-1 Structure Prediction

Predicts multi-modal molecular structures including protein complexes, ligands, and nucleic acids using the Chai-1 foundation model.

Calibrated Explanations Plugin Auditor

Audits and validates plugin implementations for the Calibrated Explanations framework to ensure compliance with architectural contracts and metadata standards.

Calibrated Explanations Plugin Audit

Audits Calibrated Explanations (CE) plugin implementations to ensure compliance with architectural contracts and registry trust rules.

CE Plugin Audit

Audits Calibrated Explanations plugin implementations to ensure compliance with registry trust rules, metadata validity, and architectural contract standards.

AlphaFold Protein Structure Validation

Validates protein designs and predicts complex structures using AlphaFold2 to ensure structural integrity and binding accuracy.

BoltzGen All-Atom Protein Design

Generates high-precision all-atom protein structures and binders using advanced diffusion models for side-chain aware design.

BindCraft Protein Binder Design

Generates high-affinity protein binders using end-to-end AlphaFold2 hallucination and rigorous structural validation.

ProteinMPNN Sequence Design

Designs optimized protein sequences from structural backbones using deep learning-based inverse folding.

SolubleMPNN Protein Design

Optimizes protein sequences for high-yield soluble expression in E. coli using specialized inverse-folding models.

Protein Design Workflow

Orchestrates end-to-end protein design pipelines from target preparation to validated structure selection.

ipSAE Binder Ranking

Ranks and evaluates protein binder designs using the ipSAE scoring function to identify high-confidence protein-protein interactions.

Agentic Workflow Discovery

Automates the discovery and implementation of autonomous AI agent patterns, including task decomposition, tool use, and memory management.

TensorFlow Data Pipeline Architect

Builds high-performance, scalable data pipelines using the tf.data API to maximize GPU and TPU utilization.

TensorFlow Model Deployment

Deploys, optimizes, and converts TensorFlow models for production environments including mobile, edge, and cloud.

Multimodal RAG Patterns

Implements advanced retrieval-augmented generation systems for images, text, and hybrid document content using CLIP and Voyage AI.

Golden Dataset Management

Protects and maintains high-quality AI/ML test datasets through robust backup, restoration, and data integrity validation.

Vinagent Agent Template

Provides a standardized boilerplate for building robust Agentic AI workflows with integrated tools, memory, and observability.