%0 Journal Article
%T Knotify+: Toward the Prediction of RNA H-Type Pseudoknots, Including Bulges and Internal Loops.
%A Makris E
%A Kolaitis A
%A Andrikos C
%A Moulos V
%A Tsanakas P
%A Pavlatos C
%J Biomolecules
%V 13
%N 2
%D 02 2023 6
%M 36830677
%F 6.064
%R 10.3390/biom13020308
%X The accurate "base pairing" in RNA molecules, which leads to the prediction of RNA secondary structures, is crucial in order to explain unknown biological operations. Recently, COVID-19, a widespread disease, has caused many deaths, affecting humanity in an unprecedented way. SARS-CoV-2, a single-stranded RNA virus, has shown the significance of analyzing these molecules and their structures. This paper aims to create a pioneering framework in the direction of predicting specific RNA structures, leveraging syntactic pattern recognition. The proposed framework, Knotify+, addresses the problem of predicting H-type pseudoknots, including bulges and internal loops, by featuring the power of context-free grammar (CFG). We combine the grammar's advantages with maximum base pairing and minimum free energy to tackle this ambiguous task in a performant way. Specifically, our proposed methodology, Knotify+, outperforms state-of-the-art frameworks with regards to its accuracy in core stems prediction. Additionally, it performs more accurately in small sequences and presents a comparable accuracy rate in larger ones, while it requires a smaller execution time compared to well-known platforms. The Knotify+ source code and implementation details are available as a public repository on GitHub.