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Biofizika. 2001 Nov-Dec;46(6):1010-21.

[Theoretical approaches for evaluation of DNA-protein interactions].

[Article in Russian]

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All-Russian Research Institute of Agricultural Biotechnology, Russian Academy of Agricultural Sciences, ul. Timiryazevskaya 42, Moscow, 127550 Russia.


The notion of the DNA-recognizing segment of a protein for three-dimensional structures of DNA-protein complexes was formalized. Algorithms for calculating two parameters, hydrogen bonds and hydrophobic contacts, that characterize the interaction of the DNA-recognizing segment of the protein with the groove DNA major were proposed. DNA-recognizing protein segments in three-dimensional structures (of complexes) were classified according to these two parameters. These data were compared with the classification of the corresponding DNA-recognizing domains according to structure. The contribution of each pair amino acid residue-base to the interaction of protein with the DNA major groove was calculated.

[Indexed for MEDLINE]

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