ArticleBMC bioinformatics2017
LCS-TA to identify similar fragments in RNA 3D structures.
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed.
- RNAdvisor 2: A unified platform for RNA 3D model quality assessment using metrics, scoring functions, and meta-metrics.Scientific reports · 2025Article
- RNAtive to recognize native-like structure in a set of RNA 3D models.Bioinformatics (Oxford, England) · 2025Article
- rsRNASP1: A distance- and dihedral-dependent statistical potential for RNA 3D structure evaluation.Biophysical journal · 2025Article
- Unknotting RNA: A method to resolve computational artifacts.PLoS computational biology · 2025Article
- Has AlphaFold3 achieved success for RNA?Acta crystallographica. Section D, Structural biology · 2025Article
- RNA-TorsionBERT: leveraging language models for RNA 3D torsion angles prediction.Bioinformatics (Oxford, England) · 2024Article
- RNAtango: Analysing and comparing RNA 3D structures via torsional angles.PLoS computational biology · 2024Article
- Knotted artifacts in predicted 3D RNA structures.PLoS computational biology · 2024Article
- When will RNA get its AlphaFold moment?Nucleic acids research · 2023Article
- RNA 3D Structure Comparison Using RNA-Puzzles Toolkit.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Article
- Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models.International journal of molecular sciences · 2022Article
- RNAspider: a webserver to analyze entanglements in RNA 3D structures.Nucleic acids research · 2022Article
- Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions.RNA (New York, N.Y.) · 2022Article
- RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools.Nucleic acids research · 2020Article
- RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures.BMC bioinformatics · 2018Article
- Discovering Structural Motifs in miRNA Precursors from theMolecules (Basel, Switzerland) · 2018Article
- New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation.Bioinformatics (Oxford, England) · 2018Article
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundIn modern structural bioinformatics, comparison of molecular structures aimed to identify and assess similarities and differences between them is one of the most commonly performed procedures. It gives the basis for evaluation of in silico predicted models. It constitutes the preliminary step in searching for structural motifs. In particular, it supports tracing the molecular evolution. Faced with an ever-increasing amount of available structural data, researchers need a range of methods enabling comparative analysis of the structures from either global or local perspective.
resultsHerein, we present a new, superposition-independent method which processes pairs of RNA 3D structures to identify their local similarities. The similarity is considered in the context of structure bending and bonds' rotation which are described by torsion angles. In the analyzed RNA structures, the method finds the longest continuous segments that show similar torsion within a user-defined threshold. The length of the segment is provided as local similarity measure. The method has been implemented as LCS-TA algorithm (Longest Continuous Segments in Torsion Angle space) and is incorporated into our MCQ4Structures application, freely available for download from http://www.cs.put.poznan.pl/tzok/mcq/ .
conclusionsThe presented approach ties torsion-angle-based method of structure analysis with the idea of local similarity identification by handling continuous 3D structure segments. The first method, implemented in MCQ4Structures, has been successfully utilized in RNA-Puzzles initiative. The second one, originally applied in Euclidean space, is a component of LGA (Local-Global Alignment) algorithm commonly used in assessing protein models submitted to CASP. This unique combination of concepts implemented in LCS-TA provides a new perspective on structure quality assessment in local and quantitative aspect. A series of computational experiments show the first results of applying our method to comparison of RNA 3D models. LCS-TA can be used for identifying strengths and weaknesses in the prediction of RNA tertiary structures.
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