Specific complexes of homeodomains with DNA are formed when the protein binds to double-stranded DNA in the B-form (along the wide groove). The classification of protein-DNA complexes and their interfaces according to physicochemical and geometric parameters is associated with solving a number of computational and statistical problems. Classification should provide information on the relationship of complexes with each other, provide an opportunity to trace their evolution and provide a basis for the formulation of recognition rules and the construction of recognition models. To solve the classification problems, it is necessary to compile a list of appropriate descriptors of the complexes and their interfaces, to conduct a multivariate statistical analysis of the data from this list. We use geometric parameters, 3DNA: a software package, of spatial DNA structures at the interfaces of 75 homeodomain-DNA complexes (PDB). This paper presents the results of a multivariate statistical analysis of “Dickerson parameters” of nitrogenous base pairs of DNA at the interfaces of homeodomain-DNA complexes.
homeodomain-DNA, "Dickerson parameters", interface, DNA deformation, classification
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