Barnaba

Barnaba analyzes nucleic acid structures and molecular dynamics trajectories to characterize RNA structural features, dynamics, and interactions.

Key Features:

• Distance Calculations: Calculates distances between three-dimensional nucleic acid structures using various metrics to compare structural conformations.
• Back-Calculation of Experimental Data: Back-calculates experimental observables from three-dimensional structures.
• Cluster Analysis and Dimensionality Reductions: Performs cluster analysis and dimensionality-reduction techniques on molecular simulation data to identify conformational states.
• Three-Dimensional Motif Search: Searches for three-dimensional motifs within Protein Data Bank (PDB) structures and trajectories.
• Elastic Network Models Construction: Constructs elastic network models for nucleic acids and nucleic acid–protein complexes to probe molecular flexibility.
• Torsion Angles and Pucker Conformations Calculation: Calculates torsion angles and pucker conformations of nucleotides.
• Base-Pairing/Base-Stacking Interaction Detection: Detects base-pairing and base-stacking interactions in nucleic acid structures.
• Visualization Capabilities: Generates graphics that visualize extended secondary structure and molecular dynamics across sets of conformations.

Scientific Applications:

• RNA dynamics and structure–function relationships: Analyzes conformational ensembles to relate sequence, structure, dynamics, and function of RNA.
• RNA folding mechanisms: Supports studies aimed at understanding RNA folding pathways through simulation analysis and structural comparison.
• RNA–protein interactions and conformational changes: Enables analysis of interactions with proteins and conformational changes during biological processes.

Methodology:

Barnaba includes support for PDB, dcd, and xtc file formats.