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Updated: Dec 20, 2025

Analyzing and Building Nucleic Acid Structures with 3DNA
Published on: April 26, 2013
TopMatch-web: pairwise matching of large assemblies of protein and nucleic acid chains in 3D
Markus Wiederstein1, Manfred J Sippl1
1Paris-Lodron-University of Salzburg, Department of Biosciences, Hellbrunner Str. 34, 5020 Salzburg, Austria.
Abstract:
Frequently, the complete functional units of biological molecules are assemblies of protein and nucleic acid chains. Stunning examples are the complex structures of ribosomes. Here, we present TopMatch-web, a computational tool for the study of the three-dimensional structure, function and evolution of such molecules. The unique feature of TopMatch is its ability to match the protein as well as nucleic acid chains of complete molecular assemblies simultaneously. The resulting structural alignments are visualized instantly using the high-performance molecular viewer NGL. We use the mitochondrial ribosomes of human and yeast as an example to demonstrate the capabilities of TopMatch-web. The service responds immediately, enabling the interactive study of many pairwise alignments of large molecular assemblies in a single session. TopMatch-web is freely accessible at https://topmatch.services.came.sbg.ac.at.
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