Amit Verma (Business), Mark Lewis (Business), and Todd Eckdahl (Biology), “Qfold: A New Modeling Paradigm for the RNA Folding Problem”

Abstract: Ribonucleic Acid (RNA) molecules play informational, structural, and metabolic roles in all living cells. RNAs are chains of nucleotides containing bases {A,C,G,U} that interact via base pairings to determine higher-order structure and functionality. The RNA folding problem is to predict one or more secondary RNA structures from a given primary sequence of bases. From a mathematical modeling perspective, solutions to the RNA folding problem come from minimizing the thermodynamic free energy of a structure by selecting which bases will be paired, subject to a set of constraints. Here we report on a Quadratic Unconstrained Binary Optimization (QUBO) modeling paradigm that fits naturally with the parameters and constraints required for RNA folding prediction. Three QUBO models are presented along with a hybrid metaheuristic algorithm. Extensive testing results show a strong positive correlation with benchmark results.