StructAlign, a program for alignment of structures of DNA–protein complexes
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.
Keywordsstructural bioinformatics DNA–protein complexes alignment web interface
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- 4.Krissinel, E., and Henrick, K. (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions, Acta Crystallogr., 60, 2256–2268.Google Scholar