Native structure-based modeling and simulation of biomolecular systems per mouse click.

Area of Science:

• Biomolecular simulations
• Computational biophysics
• Structural biology

Background:

• Molecular dynamics (MD) simulations offer atomic-level insights but face timescale and scalability challenges.
• Coarse-grained models, like native structure-based (Gō-type) models, reduce computational cost for large biomolecular systems.
• Despite successes in explaining folding and function, setting up and evaluating Gō-type models remains complex.

Purpose of the Study:

• To develop an efficient infrastructure for native structure-based models.
• To enable high-throughput simulations on remote computing resources.
• To increase the accessibility and reusability of complex simulation protocols.

Main Methods:

• Established an efficient infrastructure using GridBeans and UNICORE middleware.
• Organized simulation setup for improved comparability.
• Implemented a graphical interface for managing simulation workflows on remote resources.

Main Results:

• Enabled high-throughput simulations on remote computing resources.
• Increased comparability of simulation results through organized setup.
• Demonstrated the approach for protein folding simulations across various proteins.

Conclusions:

• Presented software enhancing the entire workflow for native structure-based simulations.
• Improved capability and accessibility of existing simulation packages.
• Expected to increase confidence and adoption of modeling in research.