DISCRETE (DMD)

DISCRETE (DMD) performs coarse-grained molecular dynamics simulations using Dynamic Mode Decomposition and a refined PACSAB/PACSB force field to model protein folding, unfolding, and aggregation in aqueous conditions.

Key Features:

• Refined Force Field: Uses a refined Coarse-Grained PACSAB/PACSB force field optimized for protein structure representation.
• Dynamic Mode Decomposition (DMD): Employs Dynamic Mode Decomposition as the computational approach for simulation.
• Protein Dynamics Representation: Represents both folded and unfolded protein states, including large proteins that challenge atomistic simulations.
• Aggregation Properties: Reproduces aggregation behavior and structural ensembles combining folded cores and intrinsically disordered regions.
• Speed and Accuracy Balance: Balances computational speed and accuracy to efficiently explore unstructured protein systems.

Scientific Applications:

• Folding/Unfolding Transitions: Simulate protein folding and unfolding transitions to study conformational changes.
• Aggregation Analysis: Analyze protein aggregation and the structural ensembles of proteins with folded and intrinsically disordered regions.
• Large Proteins and IDRs: Model large proteins and intrinsically disordered regions when atomistic simulations are impractical due to size or complexity.

Methodology:

Applies Dynamic Mode Decomposition for coarse-grained molecular dynamics and uses a refined Coarse-Grained PACSAB/PACSB force field to represent protein dynamics in aqueous conditions.