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Database of Protein-Nucleic Acid Binding Pairs at Atomic and Residue Levels

  • Byungkyu Park
  • Hyungchan Kim
  • Sangmin Lee
  • Kyungsook Han
Part of the Communications in Computer and Information Science book series (CCIS, volume 375)

Abstract

As the number of structures of protein-DNA complexes and protein-RNA complexes that have been solved has been increased substantially for the past few years, a large amount of structure data is available at several resources. However, the information on the binding sites between protein and nucleic acid is not readily available from the structure data, which consist mostly of the three-dimensional coordinates of the atoms in the complexes. A few databases constructed recently provide the information on protein-nucleic acid interface, but most of them provide binding sites on either side (protein or nucleic acid) rather than binding pairs on both sides. This paper presents a new database of protein-nucleic acid binding pairs at various levels. The binding pairs identified from an extensive analysis of protein-DNA complexes and protein-RNA complexes will provide a valuable resource for studying protein-nucleic acid interactions. The database is available at http://bclab.inha.ac.kr/dbbp .

Keywords

protein-RNA interaction protein-DNA interaction hydrogen bond 

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References

  1. 1.
    Simicevic, J., Deplancke, B.: DNA-centered approaches to characterize regulatory protein-DNA interaction complexes. Molecular Biosystems 6, 462–468 (2010)CrossRefGoogle Scholar
  2. 2.
    Moras, D.: Aminoacyl-tRNA synthetases. Current Opinion in Structural Biology 2, 138–142 (1992)CrossRefGoogle Scholar
  3. 3.
    Varani, G., Nagai, K.: RNA recognition by RNP proteins during RNA processing. Annual Review of Biophysics and Biomolecular Structure 27, 407–445 (1998)CrossRefGoogle Scholar
  4. 4.
    Lewis, B.A., Walia, R.R., Terribilini, M., Ferguson, J., Zheng, C., Honavar, V., Dobbs, D.: PRIDB: a protein-RNA interface database. Nucleic Acids Research 39, D277–D282 (2011)Google Scholar
  5. 5.
    Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The Protein Data Bank. Nucleic Acids Research 28, 235–242 (2000)CrossRefGoogle Scholar
  6. 6.
    Allers, J., Shamoo, Y.: Structure-based analysis of Protein-RNA interactions using the program ENTANGLE. Journal of Molecular Biology 311, 75–86 (2001)CrossRefGoogle Scholar
  7. 7.
    Norambuena, T., Melo, F.: The Protein-DNA Interface database. BMC Bioinformatics 11 (2010)Google Scholar
  8. 8.
    Spirin, S., Titov, M., Karyagina, A., Alexeevski, A.: NPIDB: A database of Nucleic Acids-Protein Interactions. Bioinformatics 23, 3247–3248 (2007)CrossRefGoogle Scholar
  9. 9.
    Wang, L.J., Brown, S.J.: BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences. Nucleic Acids Research 34, W243–W248 (2006)Google Scholar
  10. 10.
    Terribilini, M., Lee, J.H., Yan, C.H., Jernigan, R.L., Honavar, V., Dobbs, D.: Prediction of RNA binding sites in proteins from amino acid sequence. RNA 12, 1450–1462 (2006)CrossRefGoogle Scholar
  11. 11.
    Terribilini, M., Sander, J.D., Lee, J.H., Zaback, P., Jernigan, R.L., Honavar, V., Dobbs, D.: RNABindR: a server for analyzing and predicting RNA-binding sites in proteins. Nucleic Acids Research 35, W578–W584 (2007)Google Scholar
  12. 12.
    Elkayam, E., Kuhn, C.D., Tocilj, A., Haase, A.D., Greene, E.M., Hannon, G.J., Joshua-Tor, L.: The Structure of Human Argonaute-2 in Complex with miR-20a. Cell 150, 100–110 (2012)CrossRefGoogle Scholar
  13. 13.
    McDonald, I.K., Thornton, J.M.: Satisfying Hydrogen-Bonding Potential in Proteins. Journal of Molecular Biology 238, 777–793 (1994)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Byungkyu Park
    • 1
  • Hyungchan Kim
    • 2
  • Sangmin Lee
    • 1
  • Kyungsook Han
    • 3
  1. 1.Institute for Information and Electronics ResearchInha UniversityIncheonSouth Korea
  2. 2.Department of ChemistryInha UniversityIncheonSouth Korea
  3. 3.School of Computer Science and EngineeringInha UniversityIncheonSouth Korea

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