Russian versionEnglish version   
Volume 11   Issue 2   Year 2016
Tikhonov D.A., Kulikova L.I., Efimov A.V.

Statistical Analysis of the Internal Distances of Helical Pairs in Protein Molecules

Mathematical Biology & Bioinformatics. 2016;11(2):170-190.

doi: 10.17537/2016.11.170.



  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. Efimov A.V. L-shaped structure from two α-helices with a proline residue between them. Mol. Biol. (Moscow). 1992;26:1370–1376 (in Russ.).
  6. Efimov A.V. A new super-secondary protein structure: the α α-angle. Mol. Biol. (Moscow). 1984;18:1524–1537 (in Russ.).
  7. Finkelstein A.V. Fizika belkovykh molekul (Physics of Protein Molecules). Moscow–Izhevsk; 2014. 424 p. (in Russ.).
  8. 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.).
  9. 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”)).
  10. Miller S., Janin J., Lesk A.M., Chothia C. Interior and surfage of monomeric proteins. J. Molecular Biology. 1987;196:641–656. doi: 10.1016/0022-2836(87)90038-6
  11. Creighton T.E. Proteins. 2-nd edn. N.Y.: W.H. Freeman & Co; 1991.
  12. Stepanov V.M. Molekuliarnaia biologiia. Struktura i funktsii belkov (Molecular biology. The structure and function of proteins). Moscow; 1996. 336 p. (in Russ.).
  13. Finkelstein A.V. Molekuliarnaia biologiia (Mol. Biol. (Moscow)). 1970;11:811–819 (in Russ.).
  14. Fersht A. Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding. N.Y.: W.H. Freeman & Co; 1999.
  15. Lim V.I. Structural principles of the globular organization of protein chains. A stereochemical theory of globular protein secondary structure. J. Molecular Biology. 1974;88:857–872. doi: 10.1016/0022-2836(74)90404-5
  16. Lim V.I. Algorithm for prediction of α-helices and β-structural regions in globular proteins. J. Molecular Biology. 1974;88:873–894. doi: 10.1016/0022-2836(74)90405-7
  17. Wierenga R.K., Terpstra P., Hol W.G.S. Prediction of the occurrence of the ADP-binding βαβ-fold in proteins, using an amino acid sequence fingerprint. J. Molecular Biology. 1986;187:101–107. doi: 10.1016/0022-2836(86)90409-2
  18. 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
  19. 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
  20. Dedus FF, Kulikova LI, Pankratov AN, Tetouev RL. Klassicheskie ortogonal'nye bazisy v zadachakh analiticheskogo opisaniia i obrabotki informatsionnykh signalov (Classical Orthogonal Bases in Problems of Analytical Description of Information Signals and Their Processing). Moscow; 2004. 147 p. (in Russ.).
  21. Pankratov A.N., Gorchakov M.A., Dedus F.F., Dolotova N.S., Kulikova L.I., Makhortykh S.A., Nazipova N.N., Novikova D.A., Olshevets M.M., Pyatkov M.I., Rudnev V.R., Tetuev R.K., Filippov V.V. Spectral Analysis for identification and visualization of repeats in genetic sequences. Pattern Recognition and Image Analysis. 2009;19(4):687–692. doi: 10.1134/S105466180904018X
  22. 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
  23. 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
  24. Kabsch W. A solution for the best rotation to relate two sets of vectors. Acta Crystallographica. 1976;32:922–923. doi: 10.1107/S0567739476001873
  25. 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
  26. Legland D. MatGeom: Matlab geometry toolbox for 2D/3D geometric computing. (accessed 11 March 2016).
  27. Holland P.W., Welsch R.E. Robust regression using iteratively reweighted least-squares. Communications in Statistic – Theory and Methods. 1977;6(9):813–827. doi: 10.1080/03610927708827533
Table of Contents Original Article
Math. Biol. Bioinf.
doi: 10.17537/2016.11.170
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)
References Translation into English
Math. Biol. Bioinf.
doi: 10.17537/2019.14.t18

Full text (eng., pdf)


  Copyright IMPB RAS © 2005-2019