ModeRNA

ModeRNA performs template-based comparative modeling to predict RNA three-dimensional (3D) structures of target non-coding RNAs by leveraging structural templates and sequence alignments.

Key Features:

• Comparative Modeling Approach: Employs template-based comparative modeling that uses a user-defined sequence alignment between the target and a template RNA structure to generate 3D models.
• Template Search Functionality: Searches an internal template database to identify potential template RNA structures that share structural similarity with the target sequence.
• Comprehensive Analysis Tools: Provides tools to analyze, edit, and format RNA structure files for model refinement and downstream analysis.

Scientific Applications:

• Non-coding RNA Structural Characterization: Enables modeling of non-coding RNAs to support studies of gene regulation and RNA processing by revealing 3D structural features.
• Support for Genomics, Molecular Biology, and Biotechnology: Produces 3D models that inform functional interpretation, therapeutic strategy development, and biotechnological applications.

Methodology:

Template-based comparative modeling using a known template structure and a sequence alignment between target and template, with template identification via an internal database search and modeling guided by conserved structural features; includes analysis, editing, and formatting of RNA structure files.