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

Ya V Popov; A A Galitsyna; A V Alexeevski; A S Karyagina; S A Spirin

doi:10.1134/S0006297915110073

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

Biochemistry (Mosc). 2015 Nov;80(11):1465-8. doi: 10.1134/S0006297915110073.

Authors

Ya V Popov¹, A A Galitsyna, A V Alexeevski, A S Karyagina, S A Spirin

Affiliation

¹ Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia.

PMID: 26615437
DOI: 10.1134/S0006297915110073

Abstract

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
DNA / chemistry
DNA / metabolism*
Internet
Nucleic Acid Conformation
Protein Binding
Protein Conformation
Proteins / chemistry
Proteins / metabolism*
User-Computer Interface*

Substances

Proteins
DNA