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iPARTS: an improved tool of pairwise alignment of RNA tertiary structures

iPARTS is an improved web server for aligning two RNA 3D structures based on a structural alphabet (SA)-based approach. In particular, we first derive a Ramachandran-like diagram of RNAs by plotting nucleotides on a 2D axis using their two pseudo-torsion angles η and θ. Next, we apply the affinity p...

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Detalles Bibliográficos
Autores principales: Wang, Chih-Wei, Chen, Kun-Tze, Lu, Chin Lung
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896121/
https://www.ncbi.nlm.nih.gov/pubmed/20507908
http://dx.doi.org/10.1093/nar/gkq483
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author Wang, Chih-Wei
Chen, Kun-Tze
Lu, Chin Lung
author_facet Wang, Chih-Wei
Chen, Kun-Tze
Lu, Chin Lung
author_sort Wang, Chih-Wei
collection PubMed
description iPARTS is an improved web server for aligning two RNA 3D structures based on a structural alphabet (SA)-based approach. In particular, we first derive a Ramachandran-like diagram of RNAs by plotting nucleotides on a 2D axis using their two pseudo-torsion angles η and θ. Next, we apply the affinity propagation clustering algorithm to this η-θ plot to obtain an SA of 23-nt conformations. We finally use this SA to transform RNA 3D structures into 1D sequences of SA letters and continue to utilize classical sequence alignment methods to compare these 1D SA-encoded sequences and determine their structural similarities. iPARTS takes as input two RNA 3D structures in the PDB format and outputs their global alignment (for determining overall structural similarity), semiglobal alignments (for detecting structural motifs or substructures), local alignments (for finding locally similar substructures) and normalized local structural alignments (for identifying more similar local substructures without non-similar internal fragments), with graphical display that allows the user to visually view, rotate and enlarge the superposition of aligned RNA 3D structures. iPARTS is now available online at http://bioalgorithm.life.nctu.edu.tw/iPARTS/.
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spelling pubmed-28961212010-07-02 iPARTS: an improved tool of pairwise alignment of RNA tertiary structures Wang, Chih-Wei Chen, Kun-Tze Lu, Chin Lung Nucleic Acids Res Articles iPARTS is an improved web server for aligning two RNA 3D structures based on a structural alphabet (SA)-based approach. In particular, we first derive a Ramachandran-like diagram of RNAs by plotting nucleotides on a 2D axis using their two pseudo-torsion angles η and θ. Next, we apply the affinity propagation clustering algorithm to this η-θ plot to obtain an SA of 23-nt conformations. We finally use this SA to transform RNA 3D structures into 1D sequences of SA letters and continue to utilize classical sequence alignment methods to compare these 1D SA-encoded sequences and determine their structural similarities. iPARTS takes as input two RNA 3D structures in the PDB format and outputs their global alignment (for determining overall structural similarity), semiglobal alignments (for detecting structural motifs or substructures), local alignments (for finding locally similar substructures) and normalized local structural alignments (for identifying more similar local substructures without non-similar internal fragments), with graphical display that allows the user to visually view, rotate and enlarge the superposition of aligned RNA 3D structures. iPARTS is now available online at http://bioalgorithm.life.nctu.edu.tw/iPARTS/. Oxford University Press 2010-07-01 2010-05-27 /pmc/articles/PMC2896121/ /pubmed/20507908 http://dx.doi.org/10.1093/nar/gkq483 Text en © The Author(s) 2010. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Wang, Chih-Wei
Chen, Kun-Tze
Lu, Chin Lung
iPARTS: an improved tool of pairwise alignment of RNA tertiary structures
title iPARTS: an improved tool of pairwise alignment of RNA tertiary structures
title_full iPARTS: an improved tool of pairwise alignment of RNA tertiary structures
title_fullStr iPARTS: an improved tool of pairwise alignment of RNA tertiary structures
title_full_unstemmed iPARTS: an improved tool of pairwise alignment of RNA tertiary structures
title_short iPARTS: an improved tool of pairwise alignment of RNA tertiary structures
title_sort iparts: an improved tool of pairwise alignment of rna tertiary structures
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896121/
https://www.ncbi.nlm.nih.gov/pubmed/20507908
http://dx.doi.org/10.1093/nar/gkq483
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