PROTEAND

PROTEAND visualizes uncertainties in atomic coordinates of protein structures to represent and analyze structural variability in molecular graphics.

Key Features:

• Atomic-coordinate uncertainty visualization: Represents positional uncertainty for individual atoms in protein structures within molecular graphics.
• Ensemble stick-figure models: Displays collections of superposed and overlapped stick-figure models to depict structural ensembles and variation.
• Ellipsoids from three-dimensional Gaussian models: Renders per-atom ellipsoids derived from 3D Gaussian models and associated correlation matrices to show positional variance and atomic correlations.
• Rigid-body volume clouds: Illustrates ranges of rigid-body motion for selected substructures, such as alpha helices, using clouds of dots to represent sampled volumetric occupancy.

Scientific Applications:

• Structural comparison and variability analysis: Enables analysis and comparison of protein structures by visualizing different modes of structural variation.
• Model reliability assessment: Aids assessment of the reliability of experimental or predicted models by displaying positional uncertainty and correlations.
• Protein family studies: Facilitates investigation of variation within protein families, exemplified by application to the globin family where different display methods reveal distinct types of structural variation.

Methodology:

Superposition of structures and display of overlapped stick-figure models; computation of per-atom ellipsoids from three-dimensional Gaussian models with correlation matrices; and generation of clouds of dots to represent rigid-body volumes for selected substructures.