Online citations, reference lists, and bibliographies.
← Back to Search

StructAnalyzer - A Tool For Sequence Versus Structure Similarity Analysis.

Jakub Wiedemann, M. Milostan
Published 2016 · Biology, Medicine

Cite This
Download PDF
Analyze on Scholarcy
Share
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.
This paper references
10.1093/NAR/GKH340
MUSCLE: multiple sequence alignment with high accuracy and high throughput.
R. Edgar (2004)
10.1261/rna.049502.114
RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures.
Zhichao Miao (2015)
10.1186/1471-2105-5-113
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
R. Edgar (2004)
10.1007/s00894-010-0951-x
RNA and protein 3D structure modeling: similarities and differences
Kristian M. Rother (2011)
10.1016/bs.mie.2014.10.051
Modeling complex RNA tertiary folds with Rosetta.
C. Cheng (2015)
2014)MCQ4Structures to compute similarity of molecule structures.Central
T Zok (2014)
10.1093/nar/gkv557
RNAssess—a web server for quality assessment of RNA 3D structures
P. Lukasiak (2015)
10.1007/s10100-013-0296-5
MCQ4Structures to compute similarity of molecule structures
T. Zok (2014)
10.1093/nar/gks339
Automated 3D structure composition for large RNAs
M. Popenda (2012)
10.1093/nar/28.1.235
The Protein Data Bank
H. Berman (2000)
10.1093/nar/gkt318
RNAlyzer—novel approach for quality analysis of RNA structural models
P. Lukasiak (2013)
10.1007/S10479-009-0652-Y
Some operations research methods for analyzing protein sequences and structures
P. Lukasiak (2010)
10.1093/nar/gkr1079
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy
K. Pruitt (2012)
10.1073/pnas.0906408106
A minimal sequence code for switching protein structure and function
P. Alexander (2009)
10.1073/pnas.0703836104
Automated de novo prediction of native-like RNA tertiary structures
R. Das (2007)



This paper is referenced by
Semantic Scholar Logo Some data provided by SemanticScholar