Publications

Blue Flower

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Selected Publications

A.M. Gutin and O.V.Galzitskaia, Helix-coil transition in the simplest model of large native RNA. I. Consideration of only native helices. Biofizika (Russian), 38(1), 84-92 (1993)
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A.M. Gutin and O.V.Galzitskaia, Helix-coil transition in the simplest models of large native RNA. II. Consideration of nonspecific interactions. Biofizika (Russian), 38(1), 93-98 (1993)
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O.V. Galzitskaya, B.A. Reva and A.V. Finkelstein, Attainment of an energy minimum by a protein chain does not require a complete sorting of conformations: a computerized experiment and phenomenological theory. Molecular Biology (Russian), 28(6), 1412-1427 (1994)
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O.V. Galzitskaya and A.V. Finkelstein, Self-organization of protein chain accelerates upon stabilization of its native conformation. Numerical experiment. Molecular Biology (Russian), 29(2), 181-186 (1995)
O.V. Galzitskaya and A.V. Finkelstein, Folding of chains with random and edited sequences: similarities and differences. Protein Eng., 8(9), 883-892 (1995)
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A.V. Finkelstein and O.V. Galzitskaia, Turning speed and stability of a native structure in "random" and "edited" chains. Molecular Biology (Russian), 30(1), 145-155 (1996)
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O.V. Galzitskaya and A.V. Finkelstein, Computer simulation of secondary structure folding of random and "edited" RNA chains. J.Chem. Phys., 105(1), 319-325 (1996)
O.V. Galzitskaya and A.V. Finkelstein, A theoretical study of the dependence of rate of winding of RNA-like heteropolymers on the length of the chain. Molecular Biology (Russian), 31(3), 478-487 (1997)
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O.V. Galzitskaya, Effect of the energy of distant contacts on the time of finding the native structure for RNA-like heteropolymers. Molecular Biology (Russian), 31(3), 488-491 (1997)
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I.N. Serdiuk, O.V. Galzitskaia and A.A. Timchenko, Roughness of the globular protein surface. Biofizika (Russian), 42(6), 1197-207 (1997)
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O.V. Galzitskaia, Geometrical factor and physical reasons for its influence on the kinetic and thermodynamic properties of RNA-like heteropolymers. Fold Des., 2(3), 193-201 (1997)
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A.A. Timchenko, O.V. Galzitskaya and I.N. Serdyuk, Roughness of the globular protein surface: analysis of high resolution X-ray data. Proteins, 28(2), 194-201 (1997)
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A.A. Timchenko, O.V. Galzitskaya and I.N. Serdyuk, Roughness of the globular protein surface. JINR Rapid Communications, 4(90), 59-63 (1998)
O.V. Galzitskaya and A.V. Finkelstein, Folding rate dependence on the chain length of RNA-like heteropolymers. Fold Des., 3(2), 69-78 (1998)
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V.N. Uversky, S. Winter, O.V. Galzitskaya, L. Kittler and G. Lober, Hyperphosphorylation induces structural modification of tau-protein. FEBS Lett., 439(1-2), 21-25 (1998)
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O.V. Galzitskaya and A.V. Finkelstein, A theoretical search for folding/unfolding nuclei in three-dimensional protein structures. Proc Natl Acad Sci USA., 96(20), 11299-11304 (1999)
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V.N. Uversky, O.V. Galzitskaya, S. Winter, L. Kittler and G. Lober, Effect of hyperphosphorylation on structure of TAU protein. Tsitologiia (Russian), 41(6), 540-9 (1999)
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A.V. Skugarev, O.V. Galzitskaia and AV. Finkelstein, Search for folding nuclei in the spatial structure of proteins. Molecular Biology (Russian), 33(6), 1016-1026 (1999)
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O. Galzitskaya and A. Caflisch, Solution conformation of phakellistatin 8 investigated by molecular dynamics simulations. J Mol Graph Model., 17(1), 19-27 (1999)
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O.V. Galzitskaya, A.V. Skoogarev, D.N. Ivankov and A.V. Finkelstein, Folding nuclei in 3D protein structures. Proceedings of the Pacific Symposium on Biocomputing, 131-142 (2000)
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O.V. Galzitskaya, A.K. Surin and H. Nakamura, Optimal region of average side-chain entropy for fast protein folding. Protein Sci., 9(3), 580-586 (2000)
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O.V. Galzitskaya, J. Higo, M. Kuroda and H. Nakamura, β-hairpin folds by molecular dynamics simulations. Chemical Physics Letters, 326, 421-429 (2000)
J. Higo, O.V. Galzitskaya, S. Ono and H. Nakamura, Energy landscape of a β-hairpin peptide in explicit water studied by multicanonical molecular dynamics. Chemical Physics Letters, 337, 169-175 (2001)
O.V. Galzitskaya, D.N. Ivankov and A.V. Finkelstein, Folding nuclei in proteins. FEBS Lett., 489(2-3), 113-118 (2001)
O.V. Galzitskaya, D.N. Ivankov and A.V. Finkelstein, The state of art in steps of protein folding. Summer School "The prediction and mechanism of protein folding: from topology to intermediate states". (Chomilier,J., Labesse, G, and Sadoc, J.-F., eds.) Institute d'etudes scientifiques de Cargese, 8-19 (2001)
O.V. Galzitskaya, D.N. Ivankov and A.V. Finkelstein, Kinetics of folding nuclei formation in proteins. Molecular Biology (Russia), 35(4), 708-717 (2001)
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O.V. Galzitskaya, J. Higo and A.V. Finkelstein, α-helix and β-hairpin folding from experiment, analytical theory and molecular dynamics simulations. Current Protein and Peptide Science, 3(2), 191-200 (2002)
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O.V. Galzitskaya, Sensitivity of folding pathway to the details of amino-acid sequence. Molecular Biology (Russian), 36(3), 386-390 (2002)
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O.V. Galzitskaia, Folding of β-hairpins. Molecular Biology (Russian), 36(5), 755-760 (2002)
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K. Ikeda, O.V. Galzitskaya, H. Nakamura and J. Higo, β-hairpin, α-helices, and the intermediates among the secondary structures in the energy landscape of a peptide from a distal β-hairpin of SH3 domain. J.Comp. Chem., 24(3), 310-318 (2003)
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O.V. Galzitskaya, S.O. Garbuzynskiy, D.N. Ivankov and A.V. Finkelstein, Chain length is the main determinant of the folding rate for proteins with three-state folding kinetics. Protein, 51 (2), 162-166 (2003)
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O.V. Galzitskaya and B.S. Melnik, Prediction of protein domain boundaries from sequence alone. Protein Science, 12(4), 696-701 (2003)
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S.O. Garbuzynskiy, A.V. Finkelstein and O.V. Galzitskaya, Outlining folding nuclei in globular proteins. J. Mol. Biol., 336(2), 509-525 (2004)
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A.V. Finkelstein and O.V. Galzitskaya, Physics of protein folding. Physics of Life Reviews, 1, 23-56 (2004)
S.O. Garbuzynskiy, M.Yu. Lobanov and O.V. Galzitskaya, To be folded or to be unfolded? Protein Science, 13(11), 2871-2877 (2004)
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Sh.Suzuki, O.V. Galzitskaya, D. Mitomo and J. Higo, General dynamic properties of Aβ12-36 amyloid peptide involved in Alzheimer's disease from unfolding simulation. Eur. J. Biochem., 136(5), 583-594 (2004)
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V.V. Marchenkov, I.V. Sokolovskii, N.V. Kotova, O.V. Galzitskaya, E.S. Bochkareva, A.S. Girshovich and G.V. Semisotnov, The interaction of the GroEL chaperone with early kinetic intermediates of renaturing proteins inhibits the formation of their native structure. Biofizika (Russian), 49(6), 987-994 (2004)
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B.S. Melnik, S.O. Garbuzynskiy, M.Yu. Lobanov and O.V. Galzitskaya, The difference between protein structures that are obtained by X-ray analysis and magnetic resonance spectroscopy. Molecular Biology (Russian), 39(1), 129-38 (2005)
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A.V. Finkelstein, D.N. Ivankov and O.V. Galzitskaya, Prediction folding rates and folding nuclei in globular proteins on the basis of theory of their folding. Progress in biological chemistry (Russia), 45, 3-36 (2005)
O.V. Galzitskaya, S.O. Garbuzynskiy and A.V. Finkelstein, Theoretical study of protein folding: outlining folding nuclei and estimation of protein folding rates. Journal of Physics: Condensed Matter., 17, S1539-S1551 (2005)
S.O. Garbuzynskiy, B.S. Melnik, M.Yu.Lobanov, A.V. Finkelstein and O.V. Galzitskaya, Comparison of X-ray and NMR structures: is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures? Protein, 60(1), 139-147 (2005)
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S.O. Garbuzynskiy, A.V. Finkelstein and O.V. Galzitskaya, On prediction of folding nuclei in globular proteins. Molecular Biology (Russian), 39(6), 1032-1041 (2005)
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O.V. Galzitskaya, N.V. Dovidchenko, M.Yu. Lobanov and S.O. Garbuzynskiy, Prediction of protein domain boundaries from statistics of appearance of amino acid residues. Molecular Biology (Russian), 40(1), 111-121 (2006)
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O.V. Galzitskaya, S.O. Garbuzynskiy and M.Yu. Lobanov, Prediction of natively unfolded regions in protein chains. Molecular Biology (Russian), 40(2) 341-348 (2006)
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O.V. Galzitskaya and S.O. Garbuzynskiy, Entropy capacity determines protein folding. Protein, 63(1), 144-154 (2006)
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O.V. Galzitskaya, S.O. Garbuzynskiy and M.Yu. Lobanov, Is it possible to predict amyloidogenic regions from sequence alone? Journal of Bioinformatics and Computational Biology (JBCB), 4(2), 373-88 (2006)
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O.V. Galzitskaya and S.O. Garbuzynskiy, Optimal relationship between average conformational entropy and average energy of residue interaction for fast protein folding. Biofizika (Russia), 51(4), 622-632 (2006)
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N.S. Bogatyreva, A.V. Finkelstein and O.V. Galzitskaya, Trend of amino acid compositions of different taxa. Journal of Bioinformatics and Computational Biology (JBCB), 4(2), 597-608 (2006)
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O.V. Galzitskaya, S.O. Garbuzynskiy and M.Yu. Lobanov, A search of amyloidogenic regions in protein chain. Molecular Biology (Russian), 40(5) 910-918 (2006)
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O.V. Galzitskaya, Identification of beta-aggregate sites in protein chain. Molecular Biology (Russian), 40(6) 931-936 (2006)
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O.V. Galzitskaya, S.O. Garbuzynskiy and M.Yu. Lobanov, FoldUnfold: web server for the prediction of disordered regions in protein chain. Bioinformatic, 22(23), 2948-2949 (2006)
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O.V. Galzitskaya, S.O. Garbuzynskiy and M.Yu. Lobanov, Prediction of Amyloidogenic and Disordered Regions in Protein Chain. PLoS Computational Biology, 2(12), e177 (2006)
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M.M. Savitski, F. Kjeldsen, M.L. Nielsen, S.O. Garbuzynskiy, O.V. Galzitskaya, A.K. Surin and R.A. Zubarev, Backbone Carbonyl Group Basicities Are Related to Gas-Phase Fragmentation of Peptides and Protein Folding. Angew Chem Int Ed Engl., 46(9), 1481-1484 (2007)
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N.V. Dovidchenko, M.Yu. Lobanov and O.V. Galzitskaya, Prediction of number and position of domain boundaries in multi-domain proteins by use of amino acid sequence alone. Current Protein and Peptide Science, 8(2), 189-195 (2007)
O.V. Galzitskaya, S.O. Garbuzynskiy and M.Yu. Lobanov, Expected packing density allows predicting both amyloidogenic and disordered regions in protein chain. Journal of Physics: Condensed Matter., 19(28), 285225 (2007)
A.V. Glyakina, M.Yu. Lobanov and O.V. Galzitskaya, Search for structural factors responsible for the stability of proteins from thermophilic organisms. Molecular Biology (Russian), 41(4), 681-687 (2007)
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I.N. Serdyuk and O.V. Galzitskaya, Unstructured regions in elongation factors EF1A from three overkingdom of the living world. Molecular Biology (Russian), 41(6), 1042-1055 (2007)
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A.V. Glyakina, S.O. Garbuzynskiy, M.Yu. Lobanov and O.V. Galzitskaya, Different packing of external residues can explain differences in the thermostability of proteins from thermophilic and mesophilic organisms. Bioinformatic, 23(17), 2231-2238 (2007)
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A.V. Finkelstein, D.N. Ivankov, S.O. Garbuzynskiy and O.V. Galzitskaya, Understanding the folding rates and folding nuclei of globular proteins. Current Protein and Peptide Science, 8(6) 521-536 (2007)
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O.V. Galzitskaya, D.C. Reifsnyder, N.S. Bogatyreva, D.N. Ivankov and S.O. Garbuzynskiy, More Compact Protein Globules Exhibit Slower Folding Rates. Protein, 70(2), 329-332 (2008)
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A.V. Finkelstein, D.N. Ivankov, S.O. Garbuzynskiy and O.V. Galzitskaya, Protein structure and its folding rate. In: Applied Optimization: Mathematical Modelling of Biosystems (Editors: R.P. Mondaini, P.M. Pardalos). Springer Verlag (Heidelberg), XII, v.102, pp. 273-301 (2008)
O.V. Galzitskaya, N.S. Bogatyreva and D.N. Ivankov, Compactness determines protein folding type. J Bioinform Comput Biol., 6(4), 667-680 (2008)
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O.V. Galzitskaya, Search for folding initiation sites from amino acid sequence. J Bioinform Comput Biol., 6(4), 681-691 (2008)
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N.V. Dovidchenko and O.V. Galzitskaya, Prediction of status residue to be protected or not protected from hydrogen exchange using amino acid sequence only. The Open Biochemistry Journal, 2, 77-80 (2008)
M.Yu. Lobanov, N.S. Bogatyreva and O.V. Galzitskaya, Radius of gyration as an indicator of protein structure compactness. Molecular Biology (Russian), 42(4), 623-628 (2008)
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N.V. Dovidchenko, N.S. Bogatyreva and O.V. Galzitskaya, Prediction of loop regions in protein sequence. J Bioinform Comput Biol., 6(5), 1035-1047 (2008)
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E.I. Deruysheva, O.V. Galzitskaya and I.N. Serduyk, Prediction of short loops in the proteins with internal disorder. Molecular Biology (Russian), 42 (6), 1067--1078 (2008)
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A.V. Finkelstein, D.N. Ivankov, S.O. Garbuzynskiy and O.V. Galzitskaya, Protein structure and its folding rate. In: Applied Optimization: Mathematical Modelling of Biosystems (Editors: R.P. Mondaini, P.M. Pardalos). Springer Verlag (Heidelberg), XII, v.102, pp. 273-301 (2008)
A.V. Glyakina, O.V. Galzitskaya and N.K. Balabaev, Molecular dynamics of protein unfolding under the external forces. Bulletin of Tver University, 8(68), 109-119 (2008)
O.V. Galzitskaya, E.I. Deryusheva and I.N. Serdyuk, Phylogenetic Analysis of the Loops in Elongation Factors EF1A: Stronger Support for the Grouping of Animal and Fungi. Journal of Computer Science and System Biology., 1, 073-080 (2008)
N.S. Bogatyreva, D. N. Ivankov, M. Yu. Lobanov, O.V. Galzitskaya, Connection of shape of globular proteins with their folding and unfolding rates. Mathematical biology and bioinformatics (Russia), 3(2), 69-78 (2008)
M.Yu. Lobanov, N.S. Bogatyreva, O.V. Galzitskaya, Radius of gyration as an indicator of protein structure compactness. Molecular Biology, 42(4), 623-628 (2008)
T.S. Kalebina, T.A. Plotnikova, A.A. Gorkovskii, I.O. Selyakh, O.V. Galzitskaya, E.E. Bezsonov, G. Gellissen and I.S. Kulaev, Amyloid-like properties of Saccharomyces cerevisiae cell wall glucantransferase Bgl2p: prediction and experimental evidences. Prion, 2(2), 91-96 (2008)
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O.V. Galzitskaya, Do amyloidogenic regions intersect with folding nuclei of native structure? Proceedings from Computational biophysics to system biology (CBSB08), pp.219-221. 19-21 May, 2008b, Julich, Germany (2008)
O.V. Galzitskaya, S.O. Garbuzynskiy, Folding and aggregation features of proteins. Nova Science Publishers, Inc., In: Protein Misfolding, Editors: Cian B. O'Doherty and Adam C. Byrne, pp.99-112 (2008)
O.V. Galzitskaya, Are the same or different amino acid residues responsible for correct and incorrect protein folding? Biochemistry (Russian), 74(2), 229-237 (2009)
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J. Fong, B. Shoemaker, S.O. Garbuzynskiy, M.Yu. Lobanov, O.V. Galzitskaya and A. Panchenko, Intrinsic disorder in proteins and their complexes: a large-scale view. PLoS Comput Biol., 5(3), e1000316 (2009)
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O.V. Galzitskaya and S.O. Garbuzynskiy, Comparison of Φ-values and folding time predictions by using Monte-Carlo and Dynamic Programming approaches. Chapter in the book, "Computational Biology: New Research"., pp. 277-314 (2009)
A.V. Glyakina, N.K. Balabaev and O.V. Galzitskaya, Comparison of transition states obtained upon modeling of unfolding of immunoglobulin-binding domains of proteins L and G caused by external action with transition states obtained in the absence of force probed by experiments. Biochemistry (Russian), 74(3), 316-328 (2009)
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A. V. Glyakina, N. K. Balabaev, and O. V. Galzitskaya, Mechanical unfolding of proteins L and G with constant force: similarities and differences. J Chem. Phys., 131, 045102 (2009)
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D. N. Ivankov, N. S. Bogatyreva, M. Yu. Lobanov, O. V. Galzitskaya, Coupling between Properties of the Protein Shape and the Rate of Protein Folding. PLoS ONE, 4(8): e6476 (2009)
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A. V. Glyakina, N. K. Balabaev, and O. V. Galzitskaya, Multiple Unfolding Intermediates Obtained by Molecular Dynamic Simulations under Stretching for Immunoglobulin-Binding Domain of Protein G. Open Biochemistry, 3, 66-77 (2009)
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N.V. Dovidchenko, M.Yu., Lobanov, S.O. Garbuzynskiy, and O.V. Galzitskaya, Prediction of amino acid residues protected from hydrogen-deuterium exchange in a protein chain. Biochemistry (Russian), 74(8), 1091-1102 (2009)
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O.V. Galzitskaya, Influence of flexible loops on the rate of protein folding. Current Topics in Peptide & Protein Research, V.9, pages 71-82 (2009)
A. V. Glyakina, N. K. Balabaev, and O. V. Galzitskaya, Two-, Three-, and Four-State Events Occur in the Mechanical Unfolding of Small Protein L Using Molecular Dynamics Simulations. Protein and Peptide Letter, 17, 92-103 (2010)
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M.Yu. Lobanov, B. A. Shoemaker, S. O. Garbuzynskiy, J. H. Fong, A. R. Panchenko, O. V. Galzitskaya, ComSin: Database of protein structures in bound (Complex) and unbound (Single) states in relation to their intrinsic disorder. Nucleic Acids Research, D283-D287 (2010)
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M.Yu. Lobanov, S.O. Garbuzynskiy, O.V. Galzitskaya, Statistical analysis of unstructured amino acid residues in protein structures. Biochemistry (Russian), 75(2), 192-200 (2010)
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T.B. Mamonova, A.V. Glyakina, M.G. Kurnikova, O.V. Galzitskaya, Flexibility and mobility in Mesophilic and thermophilic homologous proteins from Molecular Dynamics and FoldUnfold Method. J Bioinform Comput Biol., 8(3), 377-394 (2010)
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A.V. Glyakina, O.V. Galzitskaya, A comparative analysis of folding pathways of thermophilic and mesophilic proteins by Monte Carlo simulations. J Bioinform Comput Biol., 8(3), 395-411 (2010)
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O.V. Galzitskaya, Estimation of protein folding rate from Monte Carlo simulations and entropy capacity. Current Protein and Peptide Science, 11 (7), in pre (2010)
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O.V. Galzitskaya, Is protein folding rate dependent on the number of folding stages? Modeling of protein folding with ferredoxin-like fold. Biochemistry (Russian), 75(6), 807-818 (2010)
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A.V. Maltsev and O.V. Galzitskaya, Formation and participation of nano-amyloids in pathogenesis of alzheimer's disease and other amyloidogenic diseases. Biochemistry (Russian), Supplement Series B: Biomedical Chemistry, 4(3), 228вЂ“236 (2010)
S. O. Garbuzynskiy, M. Yu. Lobanov and O. V. Galzitskaya, FoldAmyloid: a method of prediction of amyloidogenic regions from protein sequence. Bioinformatic, 26, 326-332 (2010)
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A.V. Glyakina, O.V. Galzitskaya, Influence of organization of native structure on its folding: modeling of the folding of alpha-helical proteins. Biochemistry (Russian), 75(8), 1098-1110 (2010)
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O.V. Galzitskaya, Influence of Conformational Entropy on the Protein Folding Rate. Entropy, 12(4), 961-982 (2010)
O. V. Galzitskaya, Modelling of Protein Folding and Prediction of Rate based on Nucleation Mechanism. Nova Science Publishers, Inc., ISBN: 978-1-61728-990-3 In: protein Folding Editor: Eric C. Walters, in press (2010)
A. V. Glyakina, O. V. Galzitskaya, N. K. Balabaev, Investigation of mechanical properties of immunoglobulin-binding properties of proteins L and G by molecular dynamics simulations. Computer research and modeling, 2, 73-81 (2010)
M. Yu. Lobanov, E. I. Furletova, N. S. Bogatyreva, M. A. Roytberg, O. V. Galzitskaya, Library of Disordered Patterns in 3D Protein Structures. PLoS Computational Biology, 6(10):e1000958. (2010)
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Galzitskaya O.V., Lobanov M. Yu., Finkelstein A.V., Cunning simplicity of a stoichiometry driven protein folding thesis. J. Biomol. Struct. Dyn., 28 In pre (2010)
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O.V. Galzitskaya, N.S. Bogatyreva, A.V. Glyakina, Bacterial proteins fold faster than eukaryotic proteins with simple folding kinetics. Biochemistry (Russian), In press (2010)
L.B. Pereyaslavets, M.V. Baranov, E.I. Leonova, O.V. Galzitskaya, Prediction of folding/unfolding nuclei for tRNA molecules. Biochemistry (Russian), In press (2010)

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