Biochemistry (Moscow)

, Volume 80, Issue 11, pp 1465–1468 | Cite as

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
Article

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.

Keywords

structural bioinformatics DNA–protein complexes alignment web interface 

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References

  1. 1.
    Taylor, W. R., and Orengo, C. A. (1989) Protein structure alignment, J. Mol. Biol., 208, 1–22.CrossRefPubMedGoogle Scholar
  2. 2.
    Holm, L., and Sander, C. (1993) Protein structure comparison by alignment of distant matrices, J. Mol. Biol., 233, 123–138.CrossRefPubMedGoogle Scholar
  3. 3.
    Shindiyalov, I. N., and Bourne, P. E. (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path, Protein Eng., 9, 739–747.CrossRefGoogle Scholar
  4. 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
  5. 5.
    Murzin, A. G., Brenner, S. E., Hubbard, T., and Chothia, C. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures, J. Mol. Biol., 247, 536–540.PubMedGoogle Scholar
  6. 6.
    King, D. A., Zhang, L., Guarente, L., and Marmorstein, R. (1999) Structure of a HAP1–DNA complex reveals dramatically asymmetric DNA binding by a homodimeric protein, Nat. Struct. Biol., 6, 64–71.CrossRefPubMedGoogle Scholar

Copyright information

© Pleiades Publishing, Ltd. 2015

Authors and Affiliations

  • Ya. V. Popov
    • 1
  • A. A. Galitsyna
    • 1
  • A. V. Alexeevski
    • 1
    • 2
    • 3
  • A. S. Karyagina
    • 2
    • 4
    • 5
  • S. A. Spirin
    • 1
    • 2
    • 3
  1. 1.Faculty of Bioengineering and BioinformaticsLomonosov Moscow State UniversityMoscowRussia
  2. 2.Belozersky Institute of Physico-Chemical BiologyLomonosov Moscow State UniversityMoscowRussia
  3. 3.Institute of System StudiesRussian Academy of SciencesMoscowRussia
  4. 4.Gamaleya Center of Epidemiology and MicrobiologyMoscowRussia
  5. 5.Institute of Agricultural BiotechnologyMoscowRussia

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