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Volume 12   Issue 1   Year 2017
Tikhonov D.A., Kulikova L.I., Efimov A.V.

The study of interhelical angles in the structural motifs formed by two helices

Mathematical Biology & Bioinformatics. 2017;12(1):83-101.

doi: 10.17537/2017.12.83.



  1. Efimov A.V. Standard structures in proteins. Prog. Biophys. Molec. Biol. 1993;60:201–239. doi: 10.1016/0079-6107(93)90015-C
  2. Gordeev A.B., Kargatov A.M., Efimov A.V. PCBOST: Protein classification based on structural trees. Biochemical and Biophysical Research Communications. 2010;397:470–471. doi: 10.1016/j.bbrc.2010.05.136
  3. Efimov A.V. Super-secondary structures and modeling of protein folds. In: Methods in Molecular Biology. Ed. Kister A.E. Clifton: Humana Press; 2013. V. 932. P. 177–189.
  4. Brazhnikov E.V., Efimov A.V. Structure of α-α-hairpins with short connections in globular proteins. Molecular Biology. 2001;35(1):89–97. doi: 10.1023/A:1004859003221
  5. Rudnev V.R., Pankratov A.N., Kulikova L.I., Dedus F.F., Tikhonov D.A., Efimov A.V. Recognition and Stability Analysis of Structural Motifs of α-α-corner Type in Globular Proteins. Mathematical Biology and Bioinformatics. 2013;8(2):398–406 (in Russ.). doi: 10.17537/2013.8.398
  6. Rudnev V.R., Pankratov A.N., Kulikova L.I., Dedus F.F., Tikhonov D.A., Efimov A.V. Conformational Analysis of Structural Motifs of α-α-Corner in the Computational Experiment of Molecular Dynamics. Mathematical Biology and Bioinformatics. 2014;9(2):575–584 (in Russ.). doi: 10.17537/2014.9.575
  7. Dedus F.F., Makhortykh S.A., Ustinin M.N., Dedus A.F. Obobshchennyi spektral'no – analiticheskii metod obrabotki informatsionnykh massivov. Zadachi analiza izobrazhenii i raspoznavaniia obrazov (Generalized Spectral-Analytic Method in Information Processing. Problems of Pattern Recognition and Image Analysis). Moscow; 1999. 357 p. (in Russ.).
  8. Dedus F.F., Makhortykh S.A., Ustinin M.N. Application of the Generalized Spectral-Analytic Method in Information Problems. Pattern Recognition and Image Analysis. 2002;12(4):429-437.
  9. Pankratov A.N., Tetuev R.K., Pyatkov M.I., Toigildin V.P., Popova N.N. Spectral Analytical Method of Recognition of Inexact Repeats in Character Sequences. Proceedings of the Institute for System Programming of the RAS. 2015;27(6):335–344 (in Russ.). doi: 10.15514/ISPRAS-2015-27(6)-21
  10. Finkelstein A.V. Fizika belkovykh molekul (Physics of Protein Molecules). Moscow–Izhevsk; 2014. 424 p. (in Russ.).
  11. Ptitsyn O.B., Finkelstein A.V. In: Itogi nauki i tekhniki (Results in Science and Technology). Ed. Vol'kenshtein M.D. Moscow; 1979. V. 15. P. 6–41. (Series “Molecular Bilogy”) (in Russ.).
  12. Shul'ts G.E., Shirmer R.Kh. Printsipy strukturnoi organizatsii belkov. Moscow; 1982. 354 p. (Translation of: Schulz G.E., Schirmer R.H. Principles of Protein Structure Springer-Verlag New. York, 1979. (Series “Springer Advanced Texts in Chemistry”)).
  13. Miller S., Janin J., Lesk A.M., Chothia C. Interior and surfage of monomeric proteins. MolecularBiology. 1987;196:641–656. doi: 10.1016/0022-2836(87)90038-6
  14. Creighton T.E. Proteins. N.Y.: W.H. Freeman & Co; 1991.
  15. Stepanov V.M. Molekuliarnaia biologiia. Struktura i funktsii belkov (Molecular biology. The structure and function of proteins). Moscow; 1996. 336 p. (in Russ.).
  16. Tsai F.C., Sherman J.C. Circular dichroism analysis of a synthetic peptide corresponding to the α-α-corner motif of hemoglobin. Biochemical and Biophysical Research Communications. 1993;196(1):435–439. doi: 10.1006/bbrc.1993.2268
  17. Tikhonov D.A., Kulikova L.I., Efimov A.V. Statistical Analysis of the Internal Distances of Helical Pairs in Protein Molecules. Mathematical Biology and Bioinformatics. 2016;11(2):170–190 (in Russ.). doi: 10.17537/2016.11.170
  18. 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. 2000;28:235–242. doi: 10.1093/nar/28.1.235
  19. Crick F.H.C. The Packing of a-Helices: Simple Coiled-Coils. Acta Crystallographica. 1953;6:689–697. doi: 10.1107/S0365110X53001964
  20. Lee H.S., Choi J., Yoon S. QHELIX: A Computational Tool for the Improved Measurement of Inter-Helical Angles in Proteins. Protein. 2007;26:556–561. doi: 10.1007/s10930-007-9097-9
  21. Walther D., Eisenhaber F., Argos P. Principles of Helix-Helix Packing in Proteins: The Helical Lattice Superposition Model. Molecular Biology. 1996;255:536–553. doi: 10.1006/jmbi.1996.0044
  22. Chothia C., Levitt M., Richardson D. Structure of proteins: Packing of α-helices and pleated sheets. Proc. Natl. Acad. Sci. 1977;74:4130–4134. doi: 10.1073/pnas.74.10.4130
  23. Chothia C., Levitt M., Richardson D. Helix to Helix Packing in Proteins. Molecular Biology. 1981;145:215–250. doi: 10.1016/0022-2836(81)90341-7
  24. Levitt M., Chothia C. Structural patterns in globular proteins. Nature. 1976;261:552–558. doi: 10.1038/261552a0
  25. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983;22(12):2577–2637. doi: 10.1002/bip.360221211
  26. Kabsch W. A solution for the best rotation to relate two sets of vectors. Acta Crystallographica. 1976;32:922–923. doi: 10.1107/S0567739476001873
  27. Kabsch W. A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystallographica. 1978;34:827–828. doi: 10.1107/S0567739478001680
  28. Legland D. MatGeom: Matlab geometry toolbox for 2D/3D geometric computing. (accessed 17 September 2015).
Table of Contents Original Article
Math. Biol. Bioinf.
doi: 10.17537/2017.12.83
published in Russian

Abstract (rus.)
Abstract (eng.)
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