Topology independent comparison of RNA 3D structures using the CLICK algorithm

Topology independent comparison of RNA 3D structures using the CLICK algorithm
Title:
Topology independent comparison of RNA 3D structures using the CLICK algorithm
Other Titles:
Nucleic Acids Research
Keywords:
Publication Date:
14 September 2016
Citation:
Minh N. Nguyen, Adelene Y. L. Sim, Yue Wan, M. S. Madhusudhan, Chandra Verma; Topology independent comparison of RNA 3D structures using the CLICK algorithm, Nucleic Acids Research, Volume 45, Issue 1, 9 January 2017, Pages e5, https://doi.org/10.1093/nar/gkw819
Abstract:
RNA molecules are attractive therapeutic targets because non-coding RNA molecules have increasingly been found to play key regulatory roles in the cell. Comparing and classifying RNA 3D structures yields unique insights into RNA evolution and function. With the rapid increase in the number of atomic-resolution RNA structures, it is crucial to have effective tools to classify RNA structures and to investigate them for structural similarities at different resolutions. We previously developed the algorithm CLICK to superimpose a pair of protein 3D structures by clique matching and 3D least squares fitting. In this study, we extend and optimize the CLICK algorithm to superimpose pairs of RNA 3D structures and RNA-protein complexes, independent of the associated topologies. Benchmarking Rclick on four different datasets showed that it is either comparable to or better than other structural alignment methods in terms of the extent of structural overlaps. Rclick also recognizes conformational changes between RNA structures and produces complementary alignments to maximize the extent of detectable similarity. Applying Rclick to study Ribonuclease III protein correctly aligned the RNA binding sites of RNAse III with its substrate. Rclick can be further extended to identify ligand-binding pockets in RNA. A web server is developed at http://mspc.bii.a-star.edu.sg/minhn/rclick.html.
License type:
http://creativecommons.org/licenses/by-nc/4.0/
Funding Info:
Agency for Science, Technology and Research (A*STAR) Joint Council Office (JCO) Career Development Award [15302FG145]; Biomedical Research Council (A*STAR), Singapore.
Description:
ISSN:
0305-1048
1362-4962
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