Geodesic
Recognition and Stability Analysis of Structural Motifs of $\alpha$-$\alpha$-corner Type in Globular Proteins
Matematičeskaâ biologiâ i bioinformatika, Tome 8 (2013) no. 2, pp. 398-406 
V. R. Rudnev; A. N. Pankratov; L. I. Kulikova; F. F. Dedus; D. A. Tikhonov; A. V. Efimov. Recognition and Stability Analysis of Structural Motifs of $\alpha$-$\alpha$-corner Type in Globular Proteins. Matematičeskaâ biologiâ i bioinformatika, Tome 8 (2013) no. 2, pp. 398-406. http://geodesic.mathdoc.fr/item/MBB_2013_8_2_a1/
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     author = {V. R. Rudnev and A. N. Pankratov and L. I. Kulikova and F. F. Dedus and D. A. Tikhonov and A. V. Efimov},
     title = {Recognition and {Stability} {Analysis} of {Structural} {Motifs} of $\alpha$-$\alpha$-corner {Type} in {Globular} {Proteins}},
     journal = {Matemati\v{c}eska\^a biologi\^a i bioinformatika},
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     volume = {8},
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     language = {ru},
     url = {http://geodesic.mathdoc.fr/item/MBB_2013_8_2_a1/}
}
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AU  - A. N. Pankratov
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%A A. N. Pankratov
%A L. I. Kulikova
%A F. F. Dedus
%A D. A. Tikhonov
%A A. V. Efimov
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Voir la notice de l'article provenant de la source Math-Net.Ru

The problem of recognition of structural motifs of proteins is considered by the example of $\alpha$-$\alpha$-corners. We propose a hybrid approach to solving the problems of the analysis of the spatial structure of proteins based on an analytical description of the main chain of the protein globule and spectral method for detecting repetitions. We found 110 $\alpha$-$\alpha$-corners in the PDB, corresponding to a given standard. The molecular dynamics method is shown that $\alpha$-$\alpha$-corners as autonomous entities stable in the aqueous medium.

[1] Holtje H.-D., Sippl W., Rognan D., Folkers G., Molecular Modeling. Basic Principles and Applications, Third, Revised and Expanded Edition, WILLEY-VCH Verlag GmbH Co. KGaA, 2008, 318 pp.

[2] Jonson M. S., Srinvasan N., Sowdhamini R., Blundell T. L., “Knowledge-based protein modelling”, Critical Reviews in Biochemistry and Molecular Biology, 29 (1994), 193–316

[3] Sali A., Overington M. S., Blundell T. L., “From comparisons of protein sequences and structures to protein modelling and design”, Trends in Biochemical Science, 15 (1990), 235–240 | DOI | MR

[4] Jones T. A., Thirup S., “Using known substructures in protein model building and crystallography”, EMBO Journal, 5 (1986), 819–822

[5] Dudek M. J., Scheraga H. A., “Protein structure prediction uses a combination of sequence gemology and global energy minimization”, Journal of Computational Chemistry, 11 (1990), 121–151 | DOI

[6] Rudakov K. V., Torshin I. Yu., “Voprosy razreshimosti zadachi raspoznavaniya vtorichnoi struktury belka”, Informatika i ee primeneniya, 4:2 (2010), 25–35

[7] Karasev V. A., Luchinin V. V., Sposob prognozirovaniya vtorichnoi struktury belka, , Federalnaya sluzhba po intellektualnoi sobstvennosti, patentami i tovarnym znakam (data obrascheniya: 09.04.2010) http://vector-machine.narod.ru/Description_of_patent.pdf

[8] Efimov A. V., “Standard Structures in Proteins”, Prog. Biophys. Molec. Biol., 60 (1993), 201–239 | DOI

[9] Efimov A. V., “Novaya supervtorichnaya struktura belkov: $\alpha$–$\alpha$ ugolok”, Molekulyarnaya biologiya, 18 (1984), 1524–1537

[10] 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, 19:4 (2009), 687–692 | DOI | MR

[11] Dedus F. F., Kulikova L. I., Pankratov A. N., Tetuev R. K., Klassicheskie ortogonalnye bazisy v zadachakh analiticheskogo opisaniya i obrabotki informatsionnykh signalov, uchebnoe posobie, Izdatelskii otdel VMiK MGU, M., 2004, 147 pp.

[12] Dedus F. F., Makhortykh S. A., Ustinin M. N., Dedus A. F., Obobschennyi spektralno-analiticheskii metod obrabotki informatsionnykh massivov. Zadachi analiza izobrazhenii i raspoznavaniya obrazov, Mashinostroenie, M., 1999, 357 pp.

[13] Bronshtein I. N., Semendyaev K. A., Spravochnik po matematike dlya inzhenerov i uchaschikhsya vtuzov, Nauka, M., 1980, 976 pp.

[14] Dedus F. F., Kulikova L. I., Makhortykh S. A., Nazipova N. N., Pankratov A. N., Tetuev R. K., “Analiticheskie metody raspoznavaniya povtoryayuschikhsya struktur v genomakh”, Doklady Akademii Nauk, 411:5 (2006), 599–602 | MR | Zbl

[15] Ranganathan S., Izotov D., Kraka E., Cremer D., “Description and recognition of regular and distorted secondary structures in proteins using the automated protein structure analysis method”, Proteins: Structure, Function, and Bioinformatics, 76 (2009), 418–438 | DOI