iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures

Area of Science:

• Structural Biology
• Bioinformatics
• Computational Biology

Background:

• Interactive visualization of molecular structures is crucial for understanding biological processes.
• Current tools may lack integrated views of 1D, 2D, and 3D data.
• Efficient analysis and sharing of complex molecular data are needed.

Purpose of the Study:

• To develop a web-based 3D molecular structure viewer for interactive structural analysis.
• To create a tool that integrates multiple data representations for comprehensive molecular exploration.
• To enable dynamic synchronization and sharing of molecular visualizations.

Main Methods:

• Developed iCn3D, a web-based application for 3D molecular structure visualization.
• Integrated 1D sequence/annotation browser with 2D molecular contacts and 3D structure displays.
• Implemented dynamic synchronization of selections across all display windows.
• Incorporated features for displaying biological annotations, structure-structure alignments (VAST+), and sequence-structure alignments (BLAST).
• Enabled visualization of electron density maps and export for 3D printing.

Main Results:

• iCn3D simultaneously displays 3D structure, 2D contacts, and 1D sequences with synchronized selections.
• Biological annotations (domains, variations) are shown as tracks in the 1D browser.
• Customized displays can be shared via a URL.
• Supports display of structure-structure and sequence-structure alignments.
• Can visualize electron density maps and export files for 3D printing.

Conclusions:

• iCn3D provides an integrated platform for interactive molecular structure analysis.
• The tool enhances the visualization and understanding of complex biological data.
• iCn3D facilitates collaboration and dissemination of structural information through shareable links.