3dRNA

3dRNA predicts three-dimensional RNA structures from sequence information by generating, ranking, and optimizing RNA conformations.

Key Features:

• RNA Structure Sampling: Generates diverse candidate RNA three-dimensional conformations from input RNA sequences to explore possible structural configurations.
• Structure Ranking: Evaluates and ranks sampled RNA structures based on predicted stability and structural plausibility.
• Residue–Residue Restraint Optimization: Refines predicted RNA structures through optimization procedures incorporating residue–residue interaction restraints.
• Pseudoknot Modeling: Supports modeling of RNA pseudoknots through restraint-based structural optimization.

Scientific Applications:

• RNA Structural Biology: Enables computational prediction of RNA tertiary structures for studying RNA structure–function relationships.
• Functional RNA Analysis: Supports investigation of RNA molecules involved in gene regulation, catalysis, and viral replication.
• RNA-Targeted Drug Discovery: Facilitates structural analysis of RNA targets for therapeutic development.

Methodology:

The method predicts RNA tertiary structures by sampling candidate conformations from RNA sequences, ranking predicted structures based on stability, and optimizing models using residue–residue interaction restraints to refine structural accuracy and model pseudoknots.