TriplexRNA

TriplexRNA predicts cooperating microRNA (miRNA) pairs and identifies their mutual target mRNAs as RNA triplexes, integrating miRNA target prediction, triplex structure analysis, molecular dynamics simulations, and mathematical modeling to assess repression efficiency.

Key Features:

• Prediction of Cooperating miRNA Pairs: Computational workflows predict miRNA pairs that can cooperatively repress target mRNAs.
• Identification of Mutual Target Genes: Identifies genes that are mutual targets of cooperating miRNAs, referred to as RNA triplexes.
• Integration of Multiple Analytical Methods: Integrates miRNA target prediction, triplex structure analysis, molecular dynamics simulations, and mathematical modeling.
• miRNA Target Prediction: Utilizes state-of-the-art methods for predicting potential miRNA targets.
• Triplex Structure Analysis: Assesses the structural feasibility of RNA triplex formation.
• Molecular Dynamics Simulations: Evaluates the stability and dynamics of predicted RNA triplexes using molecular dynamics simulations.
• Mathematical Modeling: Estimates the efficiency of target repression by cooperative miRNAs through mathematical modeling.

Scientific Applications:

• Mechanistic studies of miRNA cooperativity: Enables investigation of mechanisms underlying enhanced gene regulation by cooperative miRNAs.
• Target discovery in biological processes and disease: Identifies novel targets of miRNA pairs that may be relevant to specific biological processes and diseases.
• Analysis of fine-tuned gene expression: Facilitates exploration of fine-tuned gene expression patterns mediated by miRNA interactions.

Methodology:

Computational workflows explicitly include miRNA target prediction, prediction of cooperating miRNA pairs, triplex structure analysis, molecular dynamics simulations, and mathematical modeling to estimate repression efficiency.