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Volume 9   Issue 2   Year 2014
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 & Bioinformatics. 2014;9(2):575-584.

doi: 10.17537/2014.9.575.

References

  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. Brazhnikov EV, Efimov AV. Structure of α-α-hairpins with short connections in globular proteins. Molecular Biology. 2001;35(1):89-97. doi: 10.1023/A:1004859003221
  3. Efimov AV. L-shaped structure from two alpha-helices with a proline residue between them. Molekuliarnaia biologiia (Mol Biol (Mosk)). 1992;26:1370-1376 (in Russ.)
  4. Efimov AV. A new super-secondary protein structure: the alpha alpha-angle. Molekuliarnaia biologiia (Mol Biol (Mosk)). 1984;18:1524-1537 (in Russ.)
  5. Tsai FC, Sherman JC. 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
  6. Pankratov AN, Gorchakov MA, Dedus FF, Dolotova NS, Kulikova LI, Makhortykh SA, Nazipova NN, Novikova DA, Olshevets MM, Pyatkov MI, Rudnev VR, Tetuev RK, Filippov VV. 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
  7. Rudnev VR, Pankratov AN, Kulikova LI, Dedus FF, Tikhonov DA, Efimov AV. Recognition and Stability Analysis of Structural Motifs of α-α-corner Type in Globular Proteins. Matematicheskaya biologiya i bioinformatika (Mathematical Biology and Bioinformatics). 2013;8(2):98-406 (in Russ.). 10.17537/2013.8.98
  8. Case DA, Cheatham TE 3rd, Darden T, Gohlke H, Luo R, Merz KM Jr, Onufriev A, Simmerling C, Wang B, Woods RJ. The Amber biomolecular simulation programs. Journal of Computational Chemistry. 2005;26:1668-1688. doi: 10.1002/jcc.20290
  9. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. Journal of Chemical Physics. 1983;79:926-935. doi: 10.1063/1.445869
  10. Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T, Caldwell J, Wang J, Kollman P. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Journal of Computational Chemistry. 2003;24:1999-2012. doi: 10.1002/jcc.10349
  11. Lee MC, Duan Y. Distinguish protein decoys by using a scoring function based on a new Amber force field, short molecular dynamics simulations, and the generalized Born solvent model. Proteins. 2004;55:620-634. doi: 10.1002/prot.10470
  12. 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.).
Table of Contents Original Article
Math. Biol. Bioinf.
2014;9(2):575-584
doi: 10.17537/2014.9.575
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)
References

 

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