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StructAlign, a Program for Alignment of Structures of DNA–Protein Complexes

Ya. V. Popov1, A. A. Galitsyna1, A. V. Alexeevski1,2,3, A. S. Karyagina2,4,5, and S. A. Spirin1,2,3*

1Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, 119991 Moscow, Russia; fax: +7 (495) 939-4195

2Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; fax: +7 (495) 939-3181; E-mail: sas@belozersky.msu.ru

3Institute of System Studies, Russian Academy of Sciences, 117218 Moscow, Russia

4Gamaleya Center of Epidemiology and Microbiology, 123098 Moscow, Russia

5Institute of Agricultural Biotechnology, 127550 Moscow, Russia

* To whom correspondence should be addressed.

Received July 3, 2015
Comparative analysis of structures of complexes of homologous proteins with DNA is important in the analysis of DNA–protein recognition. Alignment is a necessary stage of the analysis. An alignment is a matching of amino acid residues and nucleotides of one complex to residues and nucleotides of the other. Currently, there are no programs available for aligning structures of DNA–protein complexes. We present the program StructAlign, which should fill this gap. The program inputs a pair of complexes of DNA double helix with proteins and outputs an alignment of DNA chains corresponding to the best spatial fit of the protein chains.
KEY WORDS: structural bioinformatics, DNA–protein complexes, alignment, web interface

DOI: 10.1134/S0006297915110073