For Publishers
DiscoveryMetadataPeer reviewHostingPublishing
For Researchers
JoinPublishReviewCollect
Register
Blog
About
Search
Advanced search
My ScienceOpen
Search
For Publishers
For Researchers
Blog
About
3
views
96
references
 Top references
cited by
6
    
0 reviews
 Review
0
comments
 Comment
0
recommends
+1 Recommend
0 collections
    0
    shares
      153
      similar
       All similar
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives

      review-article

      Read this article at

      ScienceOpenPublisherPMC
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Characterizing RNA structures and functions have mostly been focused on 2D, secondary and 3D, tertiary structures. Recent advances in experimental and computational techniques for probing or predicting RNA solvent accessibility make this 1D representation of tertiary structures an increasingly attractive feature to explore. Here, we provide a survey of these recent developments, which indicate the emergence of solvent accessibility as a simple 1D property, adding to secondary and tertiary structures for investigating complex structure–function relations of RNAs.

          Related collections

          Most cited references96

          • Record: found
          • Abstract: found
          • Article: not found

          Mfold web server for nucleic acid folding and hybridization prediction.

          M Zuker (2003)
          The abbreviated name, 'mfold web server', describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making use of universally available web GUIs (Graphical User Interfaces), the server circumvents the problem of portability of this software. Detailed output, in the form of structure plots with or without reliability information, single strand frequency plots and 'energy dot plots', are available for the folding of single sequences. A variety of 'bulk' servers give less information, but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/mfold. This URL will be referred to as 'MFOLDROOT'.
          Article 0 comments Cited 1125 times – based on 0 reviews     Review now
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling.

            Nicholas Ingolia, Sina Ghaemmaghami, John R S Newman … (2009)
            Techniques for systematically monitoring protein translation have lagged far behind methods for measuring messenger RNA (mRNA) levels. Here, we present a ribosome-profiling strategy that is based on the deep sequencing of ribosome-protected mRNA fragments and enables genome-wide investigation of translation with subcodon resolution. We used this technique to monitor translation in budding yeast under both rich and starvation conditions. These studies defined the protein sequences being translated and found extensive translational control in both determining absolute protein abundance and responding to environmental stress. We also observed distinct phases during translation that involve a large decrease in ribosome density going from early to late peptide elongation as well as widespread regulated initiation at non-adenine-uracil-guanine (AUG) codons. Ribosome profiling is readily adaptable to other organisms, making high-precision investigation of protein translation experimentally accessible.
            Article 0 comments Cited 701 times – based on 0 reviews     Review now
              Bookmark
              • Record: found
              • Abstract: not found
              • Article: not found

              The interpretation of protein structures: estimation of static accessibility.

              B. Lee, F Richards (1971)
              Article 0 comments Cited 397 times – based on 0 reviews     Review now
                Bookmark
                All references

                Author and article information

                Journal
                Journal ID (nlm-ta): Brief Bioinform
                Journal ID (iso-abbrev): Brief Bioinform
                Journal ID (publisher-id): bib
                Title: Briefings in Bioinformatics
                Publisher: Oxford University Press
                ISSN (Print): 1467-5463
                ISSN (Electronic): 1477-4054
                Publication date Collection: May 2022
                Publication date (Electronic): 25 March 2022
                Publication date PMC-release: 25 March 2022
                Volume: 23
                Issue: 3
                Electronic Location Identifier: bbac112
                Affiliations
                [1 ] Institute for Glycomics, Griffith University, Parklands Dr. Southport , QLD 4222, Australia
                [2 ] Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University , Brisbane, QLD 4111, Australia
                [3 ] Institute for Systems and Physical Biology, Shenzhen Bay Laboratory , Shenzhen 518055, China
                [4 ] Peking University Shenzhen Graduate School , Shenzhen 518055, China
                Author notes
                Corresponding authors: Yaoqi Zhou, Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China. Tel: +86 (755) 6275 2684; E-mail: zhouyq@ 123456szbl.ac.cn ; Jian Zhan, Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China. Tel: +86 (130) 5804 8876; E-mail: zhanjian@ 123456szbl.ac.cn
                Author information
                https://orcid.org/0000-0003-4316-5211
                https://orcid.org/0000-0002-0478-5533
                Article
                Publisher ID: bbac112
                DOI: 10.1093/bib/bbac112
                PMC ID: 9116373
                PubMed ID: 35348613
                SO-VID: 59debd35-dd9f-4950-85df-342519a7821b
                Copyright © © The Author(s) 2022. Published by Oxford University Press.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 13 December 2021
                Date revision received : 3 March 2022
                Date accepted : 4 March 2022
                Page count
                Pages: 16
                Funding
                Funded by: Australia Research Council;
                Award ID: DP180102060
                Categories
                Subject: Review
                Subject: AcademicSubjects/SCI01060

                ScienceOpen disciplines: Bioinformatics & Computational biology
                Keywords: solvent accessibility,sasa,rna,probing,rna–protein interactions
                Data availability:
                ScienceOpen disciplines: Bioinformatics & Computational biology
                Keywords: solvent accessibility, sasa, rna, probing, rna–protein interactions

                Comments

                Comment on this article

                scite_

                Similar content153

                See all similar

                Cited by6

                See all cited by

                Most referenced authors8,457

                See all reference authors