Ayla

Ayla visualizes molecular dynamics (MD) simulation data to map high-dimensional protein energy landscapes and support analysis of protein folding and molecular interactions.

Key Features:

• Interactive visual analytics: Enables exploration and navigation of large MD simulation datasets at individual and ensemble levels for detailed examination of conformational variability.
• Topological landscape visualization: Represents high-dimensional protein energy landscapes as a 2D terrain metaphor while preserving essential topological and geometric properties to reveal structural dynamics.
• Overlay analysis: Supports overlaying biochemical properties such as contact density onto the 2D terrain to correlate structural features with energetic and interaction metrics.

Scientific Applications:

• Protein folding analysis: Maps folding pathways, energy basins, and conformational states from MD simulations to characterize folding mechanisms.
• Molecular interaction analysis: Assesses contact density and other biochemical properties across conformational ensembles to identify interaction hotspots and transient contacts.
• Energy landscape exploration: Visualizes energetic and geometric relationships within large-scale MD datasets to support hypothesis generation, testing, and validation.

Methodology:

Constructs a 2D topological landscape that preserves topological and geometric properties of high-dimensional protein energy landscapes and overlays biochemical metrics such as contact density onto this terrain.