ezAlign

ezAlign converts coarse-grained molecular dynamics structures to atomistic resolution for multiscale modeling of biomolecular systems.

Key Features:

• Template Alignment: Aligns an atomistic template molecule to the coarse-grained structure.
• Position-Restraint Energy Minimization: Forces the atomistic molecule to adopt a conformation consistent with the coarse-grained molecule.
• System Assembly: Combines molecules, solvates, minimizes, and equilibrates with position restraints.
• Membrane Validation: Validated on a pure POPC membrane and compared with other popular methods to construct atomistic membranes.
• Example Systems: Includes surfactant self-assembly, membrane proteins, bacterial plasma membrane models, and human plasma membrane models.

Scientific Applications:

• Lipid Membrane Modeling: Constructs atomistic membranes from coarse-grained representations, as demonstrated with pure POPC membranes.
• Surfactant Self-Assembly: Models self-assembly processes of surfactant systems using multiscale approaches.
• Membrane Protein Systems: Enables atomistic modeling of membrane proteins embedded in lipid bilayers.
• Complex Biological Membranes: Supports construction of bacterial and human plasma membrane models with diverse lipid compositions.
• Multiscale Biomolecular Simulation: Bridges coarse-grained and atomistic resolutions for processes with disparate time and length scales in biology and complex systems.

Methodology:

ezAlign aligns an atomistic template molecule to the coarse-grained structure, performs position-restraint energy minimization to force the atomistic molecule to adopt a conformation consistent with the coarse-grained molecule, then combines molecules, solvates, minimizes, and equilibrates with position restraints.