PresRAT

PresRAT predicts bacterial small RNAs (sRNAs), their mRNA targets, and probable binding regions from sequence and structural attributes and generates and refines three-dimensional models followed by molecular dynamics simulations to analyze sRNA–mRNA interaction dynamics.

Key Features:

• Identification of sRNA Sequences: Uses primary and secondary structural attributes of RNA sequences to predict potential sRNAs from input sequences or entire bacterial genomes.
• Target Prediction: Identifies probable mRNA targets within specified bacterial chromosomes and pinpoints likely sRNA–mRNA binding regions.
• 3D Modeling and Molecular Dynamics Simulation: Builds and refines three-dimensional models of individual sRNAs and sRNA–mRNA duplexes and performs molecular dynamics simulations to analyze their structural dynamics.
• Comprehensive Database: Catalogs predicted sRNA sequences, their predicted mRNA targets, and corresponding 3D models with associated structural dynamics information.

Scientific Applications:

• Bacterial gene-regulation discovery: Facilitates identification of sRNAs and their targets across bacterial genomes and supports studies of sRNA-mediated gene regulation, including identification of 60,518 potential sRNA sequences from 54 bacterial genomes.
• Target mapping and interaction analysis: Enables mapping of 2,447 predicted mRNA targets from 13 bacterial genomes and pinpointing of likely binding regions between sRNAs and mRNAs.
• Structural and dynamic characterization: Provides 3D models and molecular dynamics data to study the structural dynamics of sRNA and sRNA–mRNA complexes and inform mechanistic hypotheses.

Methodology:

Computational prediction techniques analyze RNA sequence data for primary and secondary structural features indicative of sRNAs; target identification algorithms map sRNA–mRNA interactions; 3D model generation and refinement and molecular dynamics simulations characterize structural dynamics.