IPARTS: an Improved Tool of Pairwise Alignment of RNA Tertiary Structures

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2010 May 29

PMID 20507908

Citations 21

Authors

Chih-Wei Wang

Kun-Tze Chen

Chin Lung Lu

Affiliations

Soon will be listed here.

Abstract

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 eta and . Next, we apply the affinity propagation clustering algorithm to this eta- 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/.

Citing Articles

RNAtango: Analysing and comparing RNA 3D structures via torsional angles.

Mackowiak M, Adamczyk B, Szachniuk M, Zok T PLoS Comput Biol. 2024; 20(10):e1012500.

PMID: 39374268 PMC: 11486365. DOI: 10.1371/journal.pcbi.1012500.

A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures.

Bohdan D, Voronina V, Bujnicki J, Baulin E Nucleic Acids Res. 2023; 51(16):8367-8382.

PMID: 37471030 PMC: 10484739. DOI: 10.1093/nar/gkad605.

CircularSTAR3D: a stack-based RNA 3D structural alignment tool for circular matching.

Chen X, Zhang S Nucleic Acids Res. 2023; 51(9):e53.

PMID: 36987885 PMC: 10201423. DOI: 10.1093/nar/gkad222.

LocalSTAR3D: a local stack-based RNA 3D structural alignment tool.

Chen X, Khan N, Zhang S Nucleic Acids Res. 2020; 48(13):e77.

PMID: 32496533 PMC: 7367197. DOI: 10.1093/nar/gkaa453.

RMalign: an RNA structural alignment tool based on a novel scoring function RMscore.

Zheng J, Xie J, Hong X, Liu S BMC Genomics. 2019; 20(1):276.

PMID: 30961545 PMC: 6454663. DOI: 10.1186/s12864-019-5631-3.

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