easyAmber

easyAmber automates molecular dynamics (MD) simulations of proteins using the Amber package to predict time-dependent behaviors of molecular systems.

Key Features:

• Automation: Automates workflows from full-atom model construction through execution of production MD runs.
• Comprehensive Workflow: Supports full-atom model construction, optimization and equilibration of molecular systems, and execution of classical/conventional and accelerated MD simulations.
• Advanced Protocols: Implements advanced MD protocols to enhance simulation depth and accuracy.
• Scalability and Parallelization: Operates on desktops with gaming GPU-accelerators and on supercomputers and supports simultaneous multiple protein simulations.
• Amber Integration: Leverages the Amber package as the MD simulation engine.

Scientific Applications:

• Protein Engineering: Provides insights into conformational plasticity of functionally important regions and binding sites.
• Drug Discovery: Aids analysis of dynamic interactions between proteins and substrates or ligands to inform design and optimization of therapeutics.

Methodology:

Automated integration of MD simulation steps explicitly including full-atom model building, optimization and equilibration, and execution of classical/conventional and accelerated MD simulations using the Amber package, with support for GPU-accelerators and supercomputers to run simultaneous multiple protein simulations.