Wordom

Wordom analyzes conformational ensembles from molecular simulations to quantify atomic fluctuations, motion correlations, geometrical deformation indices, and ion-channel translocation dynamics.

Key Features:

• Atomic fluctuations and structural communication (Set 1): Computes correlations of motions to identify geometrically stable domains and a dynamically invariant core, detects changes in domain–domain separation and mutual orientation, analyzes overall fluctuations, performs functional mode analysis, and applies perturbation response scanning.
• Principal component and time-resolved analysis: Processes outputs from principal component analysis (PCA) of atomic fluctuations and performs wavelet analysis on large-scale simulations to capture temporal variations in conformational ensembles.
• Ion-channel conformational dynamics and ionic translocation (Set 2): Monitors pore radius changes, tracks water and ion fluxes, and measures functional collective motions such as receptor twisting and tilting angles relevant to ion channels.
• Geometrical indices of structural deformation (Set 3): Computes angles, perimeter, area, volume, β-sheet curvature, radial distribution functions, center-of-mass measures, and includes a ring perception module to monitor supramolecular self-assemblies.

Scientific Applications:

• Protein dynamics and stability: Analysis of atomic fluctuations and motion correlations to study conformational variability and structural stability of proteins.
• Membrane proteins and ion channels: Monitoring pore geometry, ion/water translocation, and collective motions to investigate functional mechanisms of ion channels and membrane receptors.
• Structural deformation and molecular mechanics: Calculation of geometrical indices and β-sheet curvature to examine deformation, mechanics, and interaction-driven structural changes.
• Supramolecular assemblies: Ring perception and geometric measurements to characterize formation and dynamics of supramolecular self-assemblies.

Methodology:

Computational methods include motion-correlation analysis, principal component analysis (PCA) processing, wavelet analysis, functional mode analysis, perturbation response scanning, radial distribution function and center-of-mass calculations, geometric-index computations, ring perception, and pore-radius plus ion/water flux tracking.