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A New Program for Detecting the Geometrical Core of a Set of Structures of Macromolecular Complexes

Yu. A. Vakulenko1, B. E. Nagaev1, 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, 117218 Moscow, Russia; fax: +7 (495) 719-7681

4Gamaleya Center of Epidemiology and Microbiology, 123098 Moscow, Russia; fax: +7 (495) 193-6183

5Institute of Agricultural Biotechnology, 127550 Moscow, Russia

* To whom correspondence should be addressed.

Received June 30, 2015; Revision received October 27, 2015
Comparison of structures of homological proteins often helps to understand functionally significant features of these structures. This concerns not only structures of separate protein chains, but also structures of macromolecular complexes. In particular, a comparison of complexes of homologous proteins with DNA is significant for analysis of the recognition of DNA by proteins. We present program LCore for detecting geometrical cores of a family of structures; a geometrical core is a set of amino acid residues and nucleotides that disposed similarly in all structures of the family. We describe the algorithm of the program, its web interface, and an example of its application to analysis of complexes of homeodomains with DNA.
KEY WORDS: structural bioinformatics, structures of macromolecules, macromolecular complexes, web interface

DOI: 10.1134/S0006297916040143