ATLAS

ATLAS provides a curated database of standardized all-atom molecular dynamics simulations and analyses of protein dynamic properties to characterize functional regions and uncommon dynamic behaviors.

Key Features:

• Standardized Molecular Dynamics Simulations: Contains standardized all-atom molecular dynamics simulations for a wide array of proteins to characterize protein dynamics.
• Trajectory visualization: Supplies trajectory visualization of simulation data for inspection of dynamic movements and conformational changes.
• Integration with Experimental Structures: Links simulation data with experimental structures to compare and contextualize conformational states.
• Analysis of Functional Protein Regions: Reports dynamic properties of specific functional regions, including domain limits (hinge positions) and residues involved in interactions.
• Exploration of Uncommon Dynamic Properties: Includes annotations and examples of chameleon subsequences and Dual Personality Fragments influenced by environment.

Scientific Applications:

• Protein Function Analysis: Uses dynamic data to investigate mechanisms underlying protein function.
• Drug Design and Development: Supports identification of dynamic binding sites and conformational states relevant to drug targeting.
• Structural Biology Research: Enables study of relationships between protein structure, dynamics, and function across experimental and simulated data.
• Educational Purposes: Provides example datasets and simulation cases for teaching principles of protein dynamics.

Methodology:

Standardized all-atom molecular dynamics simulations generate protein dynamic data; simulation trajectories are analyzed and presented as trajectory visualizations and integrated with experimental structures.