Wirecki, T. | bioRxiv Science

bioRxiv2023

DesiRNA: structure-based design of RNA sequences with a Monte Carlo approach

RNA sequences underpin the formation of complex and diverse structures, subsequently governing their respective functional properties. Despite the pivotal role RNA sequences play in cellular mechanisms, creating optimized sequences that can predictably fold into desired structures remains a significant challenge. We have developed DesiRNA, a versatile Python-based software tool for RNA sequence design. This program considers a comprehensive array of constraints, ranging from secondary structures (including pseudoknots) and GC content, to the distribution of dinucleotides emulating natural RNAs. Additionally, it factors in the presence or absence of specific sequence motifs and prevents or promotes oligomerization, thereby ensuring a robust and flexible design process. DesiRNA utilizes the Monte Carlo algorithm for the selection and acceptance of mutation sites. In tests on the EteRNA benchmark, DesiRNA displayed high accuracy and computational efficiency, outperforming most existing RNA design programs.

bioinformatics↗

bioRxiv2021

Structure prediction of the druggable fragments in SARS-CoV-2 untranslated regions

The outbreak of the COVID-19 pandemic has led to intensive studies of both the structure and replication mechanism of SARS-CoV-2. In spite of some secondary structure experiments being carried out, the 3D structure of the key function regions of the viral RNA has not yet been well understood. At the beginning of COVID-19 breakout, RNA-Puzzles community attempted to envisage the three-dimensional structure of 5'- and 3'-Un-Translated Regions (UTRs) of the SARS-CoV-2 genome. Here, we report the results of this prediction challenge, presenting the methodologies developed by six participating groups and discussing 100 RNA 3D models (60 models of 5'-UTR and 40 of 3'-UTR) predicted through applying both human experts and automated server approaches. We describe the original protocol for the reference-free comparative analysis of RNA 3D structures designed especially for this challenge. We elaborate on the deduced consensus structure and the reliability of the predicted structural motifs. All the computationally simulated models, as well as the development and the testing of computational tools dedicated to 3D structure analysis, are available for further study.

bioinformatics↗