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RNA Structure Prediction
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RNA Structure Prediction

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: closed (31 July 2020) | Viewed by 14398

Special Issue Editor

Dr. Sebastian Will

E-Mail Website
Guest Editor
Institute for Theoretical Chemistry, University of Vienna, Austria
Interests: algorithmic bioinformatics; bioinformatics of RNA; RNA structure prediction; RNA interaction; folding dynamics; sequence design; structure-based comparative analysis

Special Issue Information

Dear Colleagues,

The RNA structure is gaining more and more interest in biological research as researchers elucidate the tight connections between the functions and structures of non-coding RNAs and increasingly appreciate their versatile roles. Consequently, computational RNA structure prediction methods are receiving growing attention, since they fundamentally support biological research by enabling otherwise impracticable experiments in silico, mining huge amounts of bio-data and integrating computational models with experimental results. While considerable progress has been made, research on RNA structure prediction continues to be prolific and in high demand. Eventually, this will call for novel algorithms to deal with new scenarios and challenging open problems.

The Special Issue seeks original research contributions on novel computational methods and models in all areas of RNA structure prediction. Moreover, it welcomes applications of advanced RNA structure prediction methods to biological data. Thus, interesting topics comprise, but are not limited to, the following:

  • Secondary structure prediction, e.g., considering additional aspects, like complex side conditions or 3D motifs
  • The prediction of non-canonical interactions and 3D structures
  • The prediction of pseudoknots and interactions with other RNAs or proteins
  • Variations of RNA structure prediction and closely related problems
  • Dynamics of structure formation
  • Structure prediction integrating (and deconvoluting) experimental data
  • Structure prediction utilizing other auxiliary (e.g., comparative) information

Dr. Sebastian Will
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • RNA structure prediction
  • Non-coding RNAs
  • RNA secondary structure
  • RNA 3D structure
  • Prediction of RNA–RNA interactions
  • Prediction of RNA–protein interactions
  • Folding dynamics
  • Comparative structure analysis
  • Structure probing
  • Transcriptome analysis
  • Pseudoknots
  • Non-canonical base pairs

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Published Papers (4 papers)

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Research

14 pages, 2498 KiB  
Article
How Many Messenger RNAs Can Be Translated by the START Mechanism?
by Laurence Despons and Franck Martin
Int. J. Mol. Sci. 2020, 21(21), 8373; https://doi.org/10.3390/ijms21218373 - 8 Nov 2020
Cited by 2 | Viewed by 1953
Abstract
Translation initiation is a key step in the protein synthesis stage of the gene expression pathway of all living cells. In this important process, ribosomes have to accurately find the AUG start codon in order to ensure the integrity of the proteome. “Structure [...] Read more.
Translation initiation is a key step in the protein synthesis stage of the gene expression pathway of all living cells. In this important process, ribosomes have to accurately find the AUG start codon in order to ensure the integrity of the proteome. “Structure Assisted RNA Translation”, or “START”, has been proposed to use stable secondary structures located in the coding sequence to augment start site selection by steric hindrance of the progression of pre-initiation complex on messenger RNA. This implies that such structures have to be located downstream and at on optimal distance from the AUG start codon (i.e., downstream nucleotide +16). In order to assess the importance of the START mechanism in the overall mRNA translation process, we developed a bioinformatic tool to screen coding sequences for such stable structures in a 50 nucleotide-long window spanning the nucleotides from +16 to +65. We screened eight bacterial genomes and six eukaryotic genomes. We found stable structures in 0.6–2.5% of eukaryotic coding sequences. Among these, approximately half of them were structures predicted to form G-quadruplex structures. In humans, we selected 747 structures. In bacteria, the coding sequences from Gram-positive bacteria contained 2.6–4.2% stable structures, whereas the structures were less abundant in Gram-negative bacteria (0.2–2.7%). In contrast to eukaryotes, putative G-quadruplex structures are very rare in the coding sequence of bacteria. Altogether, our study reveals that the START mechanism seems to be an ancient strategy to facilitate the start codon recognition that is used in different kingdoms of life. Full article
(This article belongs to the Special Issue RNA Structure Prediction)
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11 pages, 1240 KiB  
Article
Using All-Atom Potentials to Refine RNA Structure Predictions of SARS-CoV-2 Stem Loops
by Christina Bergonzo and Andrea L. Szakal
Int. J. Mol. Sci. 2020, 21(17), 6188; https://doi.org/10.3390/ijms21176188 - 27 Aug 2020
Cited by 2 | Viewed by 2798
Abstract
A considerable amount of rapid-paced research is underway to combat the SARS-CoV-2 pandemic. In this work, we assess the 3D structure of the 5′ untranslated region of its RNA, in the hopes that stable secondary structures can be targeted, interrupted, or otherwise measured. [...] Read more.
A considerable amount of rapid-paced research is underway to combat the SARS-CoV-2 pandemic. In this work, we assess the 3D structure of the 5′ untranslated region of its RNA, in the hopes that stable secondary structures can be targeted, interrupted, or otherwise measured. To this end, we have combined molecular dynamics simulations with previous Nuclear Magnetic Resonance measurements for stem loop 2 of SARS-CoV-1 to refine 3D structure predictions of that stem loop. We find that relatively short sampling times allow for loop rearrangement from predicted structures determined in absence of water or ions, to structures better aligned with experimental data. We then use molecular dynamics to predict the refined structure of the transcription regulatory leader sequence (TRS-L) region which includes stem loop 3, and show that arrangement of the loop around exchangeable monovalent potassium can interpret the conformational equilibrium determined by in-cell dimethyl sulfate (DMS) data. Full article
(This article belongs to the Special Issue RNA Structure Prediction)
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18 pages, 612 KiB  
Article
CopomuS—Ranking Compensatory Mutations to Guide RNA-RNA Interaction Verification Experiments
by Martin Raden, Fabio Gutmann, Michael Uhl and Rolf Backofen
Int. J. Mol. Sci. 2020, 21(11), 3852; https://doi.org/10.3390/ijms21113852 - 28 May 2020
Cited by 1 | Viewed by 2421
Abstract
In silico RNA-RNA interaction prediction is widely applied to identify putative interaction partners and to assess interaction details in base pair resolution. To verify specific interactions, in vitro evidence can be obtained via compensatory mutation experiments. Unfortunately, the selection of compensatory mutations is [...] Read more.
In silico RNA-RNA interaction prediction is widely applied to identify putative interaction partners and to assess interaction details in base pair resolution. To verify specific interactions, in vitro evidence can be obtained via compensatory mutation experiments. Unfortunately, the selection of compensatory mutations is non-trivial and typically based on subjective ad hoc decisions. To support the decision process, we introduce our COmPensatOry MUtation Selector CopomuS. CopomuS evaluates the effects of mutations on RNA-RNA interaction formation using a set of objective criteria, and outputs a reliable ranking of compensatory mutation candidates. For RNA-RNA interaction assessment, the state-of-the-art IntaRNA prediction tool is applied. We investigate characteristics of successfully verified RNA-RNA interactions from the literature, which guided the design of CopomuS. Finally, we evaluate its performance based on experimentally validated compensatory mutations of prokaryotic sRNAs and their target mRNAs. CopomuS predictions highly agree with known results, making it a valuable tool to support the design of verification experiments for RNA-RNA interactions. It is part of the IntaRNA package and available as stand-alone webserver for ad hoc application. Full article
(This article belongs to the Special Issue RNA Structure Prediction)
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11 pages, 1852 KiB  
Communication
3dRNA v2.0: An Updated Web Server for RNA 3D Structure Prediction
by Jun Wang, Jian Wang, Yanzhao Huang and Yi Xiao
Int. J. Mol. Sci. 2019, 20(17), 4116; https://doi.org/10.3390/ijms20174116 - 23 Aug 2019
Cited by 89 | Viewed by 6683
Abstract
3D structures of RNAs are the basis for understanding their biological functions. However, experimentally solved RNA 3D structures are very limited in comparison with known RNA sequences up to now. Therefore, many computational methods have been proposed to solve this problem, including our [...] Read more.
3D structures of RNAs are the basis for understanding their biological functions. However, experimentally solved RNA 3D structures are very limited in comparison with known RNA sequences up to now. Therefore, many computational methods have been proposed to solve this problem, including our 3dRNA. In recent years, 3dRNA has been greatly improved by adding several important features, including structure sampling, structure ranking and structure optimization under residue-residue restraints. Particularly, the optimization procedure with restraints enables 3dRNA to treat pseudoknots in a new way. These new features of 3dRNA can greatly promote its performance and have been integrated into the 3dRNA v2.0 web server. Here we introduce these new features in the 3dRNA v2.0 web server for the users. Full article
(This article belongs to the Special Issue RNA Structure Prediction)
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