De novo discovery of structural motifs in RNA 3D structures through clustering
dc.contributor.author | Ge, Ping | |
dc.contributor.author | Islam, Shahidul | |
dc.contributor.author | Zhong, Cuncong | |
dc.contributor.author | Zhang, Shaojie | |
dc.date.accessioned | 2019-11-15T18:09:55Z | |
dc.date.available | 2019-11-15T18:09:55Z | |
dc.date.issued | 2018-03-09 | |
dc.identifier.citation | Ping Ge, Shahidul Islam, Cuncong Zhong, Shaojie Zhang, De novo discovery of structural motifs in RNA 3D structures through clustering, Nucleic Acids Research, Volume 46, Issue 9, 18 May 2018, Pages 4783–4793, https://doi.org/10.1093/nar/gky139 | en_US |
dc.identifier.uri | http://hdl.handle.net/1808/29778 | |
dc.description.abstract | As functional components in three-dimensional (3D) conformation of an RNA, the RNA structural motifs provide an easy way to associate the molecular architectures with their biological mechanisms. In the past years, many computational tools have been developed to search motif instances by using the existing knowledge of well-studied families. Recently, with the rapidly increasing number of resolved RNA 3D structures, there is an urgent need to discover novel motifs with the newly presented information. In this work, we classify all the loops in non-redundant RNA 3D structures to detect plausible RNA structural motif families by using a clustering pipeline. Compared with other clustering approaches, our method has two benefits: first, the underlying alignment algorithm is tolerant to the variations in 3D structures. Second, sophisticated downstream analysis has been performed to ensure the clusters are valid and easily applied to further research. The final clustering results contain many interesting new variants of known motif families, such as GNAA tetraloop, kink-turn, sarcin-ricin and T-loop. We have also discovered potential novel functional motifs conserved in ribosomal RNA, sgRNA, SRP RNA, riboswitch and ribozyme. | en_US |
dc.description.sponsorship | National Institute of General Medical Sciences of the National Institutes of Health (NIH NIGMS) (R01GM102515) | en_US |
dc.description.sponsorship | Funding for open access charge: NIH NIGMS [R01 GM102515] | en_US |
dc.publisher | Oxford University Press | en_US |
dc.rights | © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com | en_US |
dc.rights.uri | https://creativecommons.org/licenses/by-nc/4.0/ | en_US |
dc.title | De novo discovery of structural motifs in RNA 3D structures through clustering | en_US |
dc.type | Article | en_US |
kusw.kuauthor | Zhong, Cuncong | |
kusw.kudepartment | Electrical Engineering and Computer Science | en_US |
dc.identifier.doi | 10.1093/nar/gky139 | en_US |
dc.identifier.orcid | https://orcid.org/0000-0002-4051-5549 | en_US |
kusw.oaversion | Scholarly/refereed, author accepted manuscript | en_US |
kusw.oapolicy | This item meets KU Open Access policy criteria. | en_US |
dc.rights.accessrights | openAccess | en_US |
Files in this item
This item appears in the following Collection(s)
Except where otherwise noted, this item's license is described as: © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com