AQUA-DUCT

AQUA-DUCT analyzes trajectories of water, oxygen, carbon dioxide, organic solvents, and ions as they penetrate defined regions of protein structures to map pathways and active-site access.

Key Features:

• Versatility Across Molecules: Analyzes a wide range of molecules including water, oxygen, carbon dioxide, organic solvents, and ions.
• Integration of Pathway and Flux Analysis: Combines tunnel and pathway identification with analyses of accelerated water flux.
• Dynamic Screening of Single Molecules: Screens positions of thousands of single molecules over several thousand molecular dynamics steps to resolve trajectories.
• Active-Site Cavity Mapping: Focuses on active site cavities to provide detailed maps of molecular navigation within protein structures.

Scientific Applications:

• Protein Dynamics Studies: Explores how different molecules interact with and penetrate specific protein regions to elucidate protein function and dynamics.
• Drug Design and Discovery: Aids identification of potential drug binding access routes and supports optimization of small-molecule design for therapeutic targets.
• Biophysical Research: Supports investigations of solvation effects and ion transport mechanisms within proteins to study biophysical properties.

Methodology:

Simulates and analyzes molecular dynamics trajectories, tracks individual molecules through selected regions, and screens positions of thousands of single molecules over several thousand MD steps to identify penetration pathways and active-site cavities.