eRMSF

eRMSF performs ensemble-based root mean square fluctuation (RMSF) analyses of biomolecular systems across heterogeneous structural ensembles.

Key Features:

• Ensemble flexibility analysis: eRMSF extends RMSF calculations to ensembles from diverse sources including MD simulations, BioEmu, and AlphaFold2.
• Customizable selections: Users can customize atom, residue, or region selections for tailored analyses.
• High-resolution localized motion analysis: The approach delivers insights into localized motions and reveals dynamic regions often overlooked by single-method analyses.
• Unified framework: eRMSF provides a unified framework to evaluate residue or atomic fluctuations in both simulated and predicted structures.

Scientific Applications:

• Molecular flexibility comparison: eRMSF enables comparison of molecular flexibility and dynamics across different structural ensembles from computational or experimental sources.
• Complementary stability assessment: The tool complements global stability assessments with localized motion information.
• Dynamic region identification: eRMSF identifies dynamic regions in biomolecular systems that may be missed by single-method analyses.

Methodology:

eRMSF is built with MDAKit from MDAnalysis and performs ensemble-based RMSF calculations across heterogeneous ensembles.