AUTHOR=Zandi Kasra , Butler Gregory , Kharma Nawwaf TITLE=An Adaptive Defect Weighted Sampling Algorithm to Design Pseudoknotted RNA Secondary Structures JOURNAL=Frontiers in Genetics VOLUME=7 YEAR=2016 URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2016.00129 DOI=10.3389/fgene.2016.00129 ISSN=1664-8021 ABSTRACT=
Computational design of RNA sequences that fold into targeted secondary structures has many applications in biomedicine, nanotechnology and synthetic biology. An RNA molecule is made of different types of secondary structure elements and an important RNA element named pseudoknot plays a key role in stabilizing the functional form of the molecule. However, due to the computational complexities associated with characterizing pseudoknotted RNA structures, most of the existing RNA sequence designer algorithms generally ignore this important structural element and therefore limit their applications. In this paper we present a new algorithm to design RNA sequences for pseudoknotted secondary structures. We use