Qfold: a new modeling paradigm for the RNA folding problem

Mark W. Lewis (), Amit Verma and Todd T. Eckdahl
Additional contact information
Mark W. Lewis: Missouri Western State University
Amit Verma: Missouri Western State University
Todd T. Eckdahl: Missouri Western State University

Journal of Heuristics, 2021, vol. 27, issue 4, No 6, 695-717

Abstract: 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.

Keywords: RNA folding; Structure prediction; QUBO; Path relinking (search for similar items in EconPapers)
Date: 2021
References: View references in EconPapers View complete reference list from CitEc
Citations:

Downloads: (external link)
http://link.springer.com/10.1007/s10732-021-09471-3 Abstract (text/html)
Access to the full text of the articles in this series is restricted.

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:spr:joheur:v:27:y:2021:i:4:d:10.1007_s10732-021-09471-3

Ordering information: This journal article can be ordered from
http://www.springer.com/journal/10732

DOI: 10.1007/s10732-021-09471-3

Access Statistics for this article

Journal of Heuristics is currently edited by Manuel Laguna

More articles in Journal of Heuristics from Springer
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().