RiboVision

RiboVision 2.0 is a comprehensive webserver suite designed for visualization and analysis of ribosomal RNA structures. Developed at the Center for the Origins of Life at Georgia Institute of Technology, RiboVision integrates phylogenetic, structural, and evolutionary information about ribosomes, enabling researchers to explore ribosomal RNA in multiple dimensions.

Overview

RiboVision provides an integrated platform for exploring ribosomal RNA through multiple complementary views:

• Phylogenetic organization: Browse 152 species from the DESIRE database with taxonomic hierarchy
• 2D topology: Interactive secondary structure diagrams with R2DT-based layouts
• 3D structures: MolStar-based viewer for exploring atomic-level ribosome structures
• Multiple sequence alignments: Compare sequences across species with MSAViewer
• Evolutionary data: Map conservation, entropy, and functional annotations onto structures

Key Features

Visualization Tools

• Phylogenetic Browser: Navigate ribosomal RNA sequences organized by phylogenetic relationships
• 2D RNA Topology Viewer: Explore secondary structures with base pairing and stacking interactions
• 3D Structure Viewer: Interactive MolStar-based visualization of ribosome atomic structures
• Alignment Viewer: Examine multiple sequence alignments with gap-adjusted frequencies

Data Analysis

• Shannon Entropy: Calculate and visualize sequence conservation across alignments
• TwinCons: Compare two phylogenetic groups using substitution matrix-based scoring
• Nucleotide Frequencies: Analyze base composition with gap-adjusted probabilities
• RNA-Protein Contacts: Identify interactions between rRNA and ribosomal proteins (3.5Å cutoff)
• Chemical Modifications: View post-transcriptional modifications from PDB data

Structural Annotations

• Helix Definitions: Contiguous base-paired or stacked regions from Petrov et al. 2014
• Expansion Segments: Evolutionary accretion features from PNAS 2014-2015 studies
• FR3D Base Pairs: Leontis-Westhof notation for base pairing interactions

User Upload Mode

• Upload custom 3D structures (PDB or CIF format)
• Provide custom alignments for mapping
• Visualize user data with RiboVision’s analysis tools

Data Sources

RiboVision integrates data from multiple authoritative sources:

• Sequences: NCBI, UniProt, RNAcentral (152 species from DESIRE dataset)
• Phylogeny: Tree topology from Banfield lab
• 3D Structures: RCSB PDB via coordinate server API
• 2D Layouts: EMBL-EBI PDBe API with R2DT secondary structures
• Alignments: Generated using DESIRE methodology
• Base Pairs: FR3D annotations from RNA 3D Hub

Color Schemes

RiboVision employs matplotlib-based colormaps for data visualization:

• Single continuum: Viridis and rainbow colormaps for entropy, helices, and custom data
• Diverging: Blue-White-Red for TwinCons comparisons
• All colormaps exported to JavaScript using js-colormaps package

Technical Implementation

• License: MIT license
• Frontend: React-based interface with custom viewers
• RNA Topology: Modified PDBe RNA viewer
• MSA Visualization: Modified react-msa-viewer
• 3D Rendering: MolStar viewer with custom color wrapper
• Sequence Processing: BioPython for parsing and frequency calculations
• Alignment Mapping: MAFFT for sequence-alignment mapping

Contributors

RiboVision 2 was developed by Holly McCann, Caeden Meade, and Anton S. Petrov at the Center for the Origins of Life, Georgia Institute of Technology, under the direction of Loren Dean Williams. Additional contributors include Petar I. Penev and Biswajit Banerjee.

Funding

This work was funded by NASA grant 80NSSC18K1139 awarded to Loren Dean Williams and Anton S. Petrov.

Contact

For questions about RiboVision 2, contact: RiboZones@gmail.com

RiboVision complements ProteoVision, a companion tool for visualizing ribosomal proteins.