ALADYN

ALADYN aligns pairs of protein structures by comparing their internal dynamics to identify regions with similar large-scale movements associated with functional conformational changes.

Key Features:

• Dynamics-Based Alignment: Aligns protein structures by comparing patterns of internal dynamics to detect regions with similar large-scale movements linked to function.
• Elastic Network Model (ENM): Uses an elastic network model to calculate patterns of structural fluctuations within each protein at the atomic level.
• Optimal Positioning: Determines the optimal relative positioning of two protein structures by maximizing the similarity between their dynamic patterns.
• Quantitative Indicators and Data Export: Provides quantitative indicators assessing alignment quality and produces data files for downstream analysis.

Scientific Applications:

• Functional Annotation: Highlights dynamic correspondences to identify functionally similar regions across different protein families.
• Protein Engineering: Informs protein engineering efforts by revealing dynamic behaviors relevant to function and stability.
• Drug Design: Provides insights into flexible regions involved in ligand binding and enzyme activity relevant to rational drug design.

Methodology:

Accepts structure files for two proteins, computes structural fluctuations using an elastic network model that simulates atomic interactions under physiological conditions, and finds the relative orientation that maximizes similarity between the resulting dynamic patterns.