RMSX and Flipbook

RMSX and Flipbook generate residue-resolved structural motion summaries from molecular dynamics simulation trajectories, enabling quantitative, high-resolution interrogation of biomolecular dynamics through time-series motion metrics and color- and thickness-encoded protein snapshots.

Key Features:

• RMSX (time-series RMSF extension): Computes per-residue motion metrics over partitions of the original simulation rather than its entirety, pinpointing both the degree of fluctuation and when significant motion takes place for any amino acid residue.
• Flipbook visualization engine: Maps time-series, residue-level data onto structural, atomistic snapshots, coloring and scaling amino acids according to input values including RMSX or other user-provided metrics.
• Multiple output formats: Produces static flipbook panels or interactive displays for publication, presentation, and exploratory analysis.
• General-purpose input capability: Accepts RMSX values or other user-provided time-series, residue-level values for visualization.

Scientific Applications:

• Transient and localized motion detection: Identifies when and where proteins undergo conformational rearrangement, particularly for motions that are challenging to detect with traditional RMSF analysis.
• Ubiquitin dynamics analysis: Demonstrates utility on unbiased and steered molecular dynamics simulations of ubiquitin.
• HIV-1 protease dynamics analysis: Demonstrates utility on unbiased and steered molecular dynamics simulations of HIV-1 protease.
• Bacterial adhesion protein analysis: Demonstrates utility on unbiased and steered molecular dynamics simulations of the bacterial adhesion protein SdrG.

Methodology:

RMSX extends root-mean-square fluctuation (RMSF) to a time-series analysis performed over partitions of the original simulation. Flipbook transforms time-series, residue-level data into colored 3D structures by mapping simulation metrics onto structural, atomistic snapshots.