POLYVIEW-MM

POLYVIEW-MM visualizes and analyzes macromolecular structure and dynamics by generating high-quality animations and integrating structural and sequence annotations from molecular dynamics trajectories, protein structure prediction, small-molecule docking, and structural databases.

Key Features:

• Animation of Molecular Motion: Animates trajectories from molecular dynamics simulations and visualizes alternative conformers generated by protein structure prediction methods and small-molecule docking.
• Interactive Structural Visualization (Jmol): Employs Jmol with tailored extensions for interactive exploration and analysis of conformational changes.
• Publication-Quality Rendering (PyMol): Generates publication-quality animations and renderings using PyMol.
• Customizable 2D Summary Plots: Produces two-dimensional summary plots that depict changes in secondary structure states and relative solvent accessibility of individual residues.
• Structural Annotations Integration: Integrates annotations including automated mapping of interaction sites from structural homologs, and identification of cavities, ligand binding sites, transmembrane regions, and protein domains.
• Protein Sequence Annotations: Generates sequence-level annotations including secondary structure, relative solvent accessibility, functional motifs, and polymorphic sites for known and predicted structures.
• Customizable Graphical Representations: Exports two-dimensional graphical representations in customizable formats for publication and proteomic online resources.

Scientific Applications:

• Protein dynamics analysis: Investigation of conformational changes and dynamic behavior from MD trajectories and conformer ensembles.
• Ligand interaction and binding-site analysis: Identification and visualization of cavities and ligand binding sites and their dynamic context.
• Structure annotation and interpretation: Integration of structural homolog mappings, transmembrane regions, domains, and sequence annotations to support functional interpretation of known and predicted structures.

Methodology:

Animation of MD trajectories and conformers from protein structure prediction and small-molecule docking; visualization via Jmol with tailored extensions and rendering via PyMol; generation of 2D plots of secondary structure and relative solvent accessibility; automated mapping of interaction sites from structural homologs and identification of cavities, ligand binding sites, transmembrane regions, and protein domains; and generation of sequence annotations (secondary structure, relative solvent accessibility, functional motifs, polymorphic sites) integrating data from structural databases and web resources.