Chimera

Chimera provides visualization and analysis of molecular structures, density maps, sequence alignments, docking results, trajectories, and conformational ensembles to support structural biology investigations.

Key Features:

• Modular Architecture: A core plus extensions architecture enables extensible visualization and analysis functionality.
• Multiscale Visualization: A multiscale extension supports visualization of large-scale molecular assemblies such as viral coats and ribosomal subunits and provides cartoon representations.
• Sequence-Structure Integration: Integrates sequence data with structural information, enabling mapping of sequence-conserved residues to structures and adjustment of alignments based on spatial fit.
• Structure Superposition without Pre-existing Alignments: Implements a method for superimposing structures by leveraging both sequence and secondary structure information.
• Nucleic Acid Visualization: An extension computes and displays sugar puckers, base geometries, and backbone representations for nucleic acids.
• Density, Docking, and Trajectory Analysis: Supports analysis and visualization of density maps, docking results, molecular trajectories, and conformational ensembles.
• Web Services Integration (Opal): Integrates Opal toolkit web services to access computationally intensive tasks and database searches.
• Image and Animation Rendering: Generates publication-quality images and animations for examination and presentation of molecular systems.

Scientific Applications:

• Protein structure–function analysis: Comparing related structures and mapping conserved residues to infer structural determinants of function.
• Nucleic acid structural analysis: Examining sugar puckers, base geometries, and backbone conformations in RNA and DNA structures.
• Supramolecular assembly analysis: Visualization and analysis of large assemblies such as ribosomal subunits and virus capsids.
• Docking and interaction studies: Evaluation and visualization of docking results and conformational ensembles to study molecular interactions.
• Trajectory analysis: Analysis and visualization of molecular dynamics trajectories.

Methodology:

Modular core with extension framework; multiscale rendering for large assemblies; sequence-structure mapping using sequence-conserved residues and spatial-fit adjustments; a superposition method leveraging sequence and secondary structure; nucleic-acid-specific geometry computations (sugar pucker, base geometry, backbone); and Opal-based web service integration for remote computation and database searches.