StructAnalyzer - a tool for sequence versus structure similarity analysis

• Authors: Jakub Wiedemann , Maciej Miłostan
• Languages of publication: EN

Abstracts

EN

In the world of RNAs and proteins, similarities at the level of primary structures of two comparable molecules usually correspond to structural similarities at the tertiary level. In other words, measures of sequence and structure similarities are in general correlated - a high value of sequence similarity imposes a high value of structural similarity. However, important exceptions that stay in contrast to this general rule can be identified. It is possible to find similar structures with very different sequences, as well as similar sequences with very different structures. In this paper, we focus our attention on the latter case and propose a tool, called StructAnalyzer, supporting analysis of relations between the sequence and structure similarities. Recognition of tertiary structure diversity of molecules with very similar primary structures may be the key for better understanding of mechanisms influencing folding of RNAs or proteins, and as a result for better understanding of their function. StructAnalyzer allows exploration and visualization of structural diversity in relation to sequence similarity. We show how this tool can be used to screen RNA structures in Protein Data Bank (PDB) for sequences with structural variants.

Keywords

EN

sequence similarity; structural similarity; RNA

• Publisher: Polish Biochemical Society
• Journal: Acta Biochimica Polonica
• Year: 2016
• Volume: 63
• Issue: 4
• Pages: 753-757

Dates

published

2016

received

2016-05-30

revised

2016-06-28

accepted

2016-07-19

(unknown)

2016-11-02

Contributors

author

Jakub Wiedemann

• Institute of Computing Science, Poznan University of Technology, Poznań, Poland

author

Maciej Miłostan

• Institute of Computing Science, Poznan University of Technology, Poznań, Poland
• Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland

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Identifiers

DOI

10.18388/abp.2016_1333