Getting Started with Chiral Potter

Welcome to Chiral Potter, the integrated computational drug discovery platform. This guide helps you understand the core applications and analysis tools available.

Platform Overview

Chiral Potter integrates cutting-edge molecular modeling applications with automated analysis and reporting tools.

Core Applications

Structure Prediction

  • Boltz-2: Protein structure prediction with confidence scoring

Molecular Docking

  • DiffDock: Small molecule docking
  • DiffDock-PP: Protein-protein complex prediction
  • AutoDock Vina: Classical high-throughput screening

Molecular Dynamics

  • GROMACS: MD simulation and trajectory analysis

Visualization

  • Mol*: Interactive 3D molecular visualization

Analysis & Reporting

Each application includes automated analysis tools:

  • Boltz-2 Report: Structure prediction quality assessment
  • Docking Report: Binding analysis with CAPRI metrics and affinity classification
  • GROMACS Report: MD trajectory analysis with quality scoring

Getting Started

Learn the Platform

  • Applications: Explore molecular modeling tools
  • Features: Understand analysis and reporting capabilities
  • Tutorials: Follow complete workflow examples

Workflow Examples

  • Antibody-Antigen Analysis: End-to-end AI workflow from sequence to binding analysis
  • Structure Prediction: Boltz-2 workflows with confidence assessment
  • Virtual Screening: High-throughput compound screening with real metrics

Key Workflow Types

Structure-Based Design

  1. Predict structures with Boltz-2
  2. Dock compounds with DiffDock or AutoDock Vina
  3. Validate with GROMACS MD simulations
  4. Analyze with automated reporting tools

Protein Complex Analysis

  1. Predict or prepare protein structures
  2. Model complexes with DiffDock-PP
  3. Assess binding with CAPRI metrics
  4. Visualize with Mol* integration

Each workflow generates interactive HTML reports with publication-ready analysis and visualization.

Start with the tutorials to see complete workflows in action, then explore individual applications for detailed capabilities.