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Analyzing and Building Nucleic Acid Structures with 3DNA
Published on: April 26, 2013
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ARTEM server: an online tool for nucleic acid 3D motif searches, 3D structure superposition and structure-based
Dominik Sordyl1, Jan Cielesz1, Davyd R Bohdan1
1Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland.
Nucleic Acids Research
|May 5, 2026
Summary
ARTEM Server provides advanced tools for analyzing nucleic acid 3D structures, identifying local motifs and global folds. It excels at detecting structural similarities, outperforming other methods in complex cases.
Area of Science:
- Structural Biology
- Bioinformatics
- Computational Biology
Background:
- Comparative analysis of nucleic acid 3D structures is crucial for understanding function.
- Existing methods often struggle with diverse backbone contexts and sequence-independent comparisons.
Purpose of the Study:
- To present ARTEM Server, a unified platform for nucleic acid 3D structure analysis.
- To enable identification of local tertiary motifs and global fold similarities.
Main Methods:
- ARTEM Server integrates ARTEM (local motif search) and ARTEMIS (global structure alignment).
- ARTEM identifies isosteric structural arrangements independent of sequence or connectivity.
- ARTEMIS performs rigid-body superposition for sequence-ordered and permuted alignments.
Main Results:
- ARTEM and ARTEMIS demonstrate superior performance compared to existing tools.
- The methods effectively detect 3D motif and fold similarities across varied backbone structures.
- The server handles diverse inputs and provides interactive visualization and data export.
Conclusions:
- ARTEM Server offers a user-friendly web environment for exploring nucleic acid structures.
- The platform facilitates robust structural searches, overcoming limitations of sequence-dependent methods.
