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Alexey Shaytan - Publications

Affiliations: 
2013-2017 Moscow State University, Moskva, Moscow, Russia 
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59 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2025 Amaro RE, Åqvist J, Bahar I, Battistini F, Bellaiche A, Beltran D, Biggin PC, Bonomi M, Bowman GR, Bryce RA, Bussi G, Carloni P, Case DA, Cavalli A, Chang CA, ... ... Shaytan AK, et al. The need to implement FAIR principles in biomolecular simulations. Nature Methods. PMID 40175561 DOI: 10.1038/s41592-025-02635-0  0.503
2025 Armeev GA, Moiseenko AV, Motorin NA, Afonin DA, Zhao L, Vasilev VA, Oleinikov PD, Glukhov GS, Peters GS, Studitsky VM, Feofanov AV, Shaytan AK, Shi X, Sokolova OS. Structure and dynamics of a nucleosome core particle based on Widom 603 DNA sequence. Structure (London, England : 1993). PMID 40101710 DOI: 10.1016/j.str.2025.02.007  0.389
2024 Kosarim NA, Fedulova AS, Shariafetdinova AS, Armeev GA, Shaytan AK. Molecular Dynamics Simulations of Nucleosomes Containing Histone Variant H2A.J. International Journal of Molecular Sciences. 25. PMID 39596203 DOI: 10.3390/ijms252212136  0.451
2023 Oleinikov PD, Fedulova AS, Armeev GA, Motorin NA, Singh-Palchevskaia L, Sivkina AL, Feskin PG, Glukhov GS, Afonin DA, Komarova GA, Kirpichnikov MP, Studitsky VM, Feofanov AV, Shaytan AK. Interactions of Nucleosomes with Acidic Patch-Binding Peptides: A Combined Structural Bioinformatics, Molecular Modeling, Fluorescence Polarization, and Single-Molecule FRET Study. International Journal of Molecular Sciences. 24. PMID 37894874 DOI: 10.3390/ijms242015194  0.343
2023 Stefanova ME, Volokh OI, Chertkov OV, Armeev GA, Shaytan AK, Feofanov AV, Kirpichnikov MP, Sokolova OS, Studitsky VM. Structure and Dynamics of Compact Dinucleosomes: Analysis by Electron Microscopy and spFRET. International Journal of Molecular Sciences. 24. PMID 37569503 DOI: 10.3390/ijms241512127  0.403
2023 Shi X, Nordenskiöld L, Sokolova OS, Shaytan AK. Editorial: Recent advances in molecular properties of DNA-protein interactions, chromatin and their biological roles. Frontiers in Molecular Biosciences. 10: 1171714. PMID 36959980 DOI: 10.3389/fmolb.2023.1171714  0.359
2022 Armeev GA, Gribkova AK, Shaytan AK. Nucleosomes and their complexes in the cryoEM era: Trends and limitations. Frontiers in Molecular Biosciences. 9: 1070489. PMID 36504712 DOI: 10.3389/fmolb.2022.1070489  0.361
2022 Seal RL, Denny P, Bruford EA, Gribkova AK, Landsman D, Marzluff WF, McAndrews M, Panchenko AR, Shaytan AK, Talbert PB. A standardized nomenclature for mammalian histone genes. Epigenetics & Chromatin. 15: 34. PMID 36180920 DOI: 10.1186/s13072-022-00467-2  0.62
2022 Kniazeva AS, Armeev GA, Shaytan AK. H2A-H2B Histone Dimer Plasticity and Its Functional Implications. Cells. 11. PMID 36139412 DOI: 10.3390/cells11182837  0.466
2022 Gerasimova NS, Volokh OI, Pestov NA, Armeev GA, Kirpichnikov MP, Shaytan AK, Sokolova OS, Studitsky VM. Structure of an Intranucleosomal DNA Loop That Senses DNA Damage during Transcription. Cells. 11. PMID 36078089 DOI: 10.3390/cells11172678  0.327
2022 Chang HW, Feofanov AV, Lyubitelev AV, Armeev GA, Kotova EY, Hsieh FK, Kirpichnikov MP, Shaytan AK, Studitsky VM. N-Terminal Tails of Histones H2A and H2B Differentially Affect Transcription by RNA Polymerase II In Vitro. Cells. 11. PMID 36010552 DOI: 10.3390/cells11162475  0.392
2022 Sivkina AL, Karlova MG, Valieva ME, McCullough LL, Formosa T, Shaytan AK, Feofanov AV, Kirpichnikov MP, Sokolova OS, Studitsky VM. Electron microscopy analysis of ATP-independent nucleosome unfolding by FACT. Communications Biology. 5: 2. PMID 35013515 DOI: 10.1038/s42003-021-02948-8  0.363
2021 Armeev GA, Kniazeva AS, Komarova GA, Kirpichnikov MP, Shaytan AK. Histone dynamics mediate DNA unwrapping and sliding in nucleosomes. Nature Communications. 12: 2387. PMID 33888707 DOI: 10.1038/s41467-021-22636-9  0.475
2021 Espiritu D, Gribkova AK, Gupta S, Shaytan AK, Panchenko AR. Molecular Mechanisms of Oncogenesis through the Lens of Nucleosomes and Histones. The Journal of Physical Chemistry. B. PMID 33769808 DOI: 10.1021/acs.jpcb.1c00694  0.676
2020 Novikov R, Armeev G, Gribkova A, Kacher J, Gluhov G, Shaytan A. Detecting Cas9-sgRNA Complex Interactions with DNA via Fluorescent Microscopy: Computer Simulations of Experimental Designs Microscopy and Microanalysis. 1-3. DOI: 10.1017/S1431927620014166  0.334
2020 Armeev G, Panchenko A, Feofanov A, Shaytan AK. Integrative Modeling of Nucleosomes and Supranucleosomal Structures Biophysical Journal. 118. DOI: 10.1016/J.Bpj.2019.11.527  0.554
2019 Hada A, Hota SK, Luo J, Lin YC, Kale S, Shaytan AK, Bhardwaj SK, Persinger J, Ranish J, Panchenko AR, Bartholomew B. Histone Octamer Structure Is Altered Early in ISW2 ATP-Dependent Nucleosome Remodeling. Cell Reports. 28: 282-294.e6. PMID 31269447 DOI: 10.1016/J.Celrep.2019.05.106  0.74
2019 Armeev GA, Gribkova AK, Pospelova I, Komarova GA, Shaytan AK. Linking chromatin composition and structural dynamics at the nucleosome level. Current Opinion in Structural Biology. 56: 46-55. PMID 30529788 DOI: 10.1016/j.sbi.2018.11.006  0.459
2019 Bass MV, Armeev GA, Shaitan KV, Shaytan AK. The Effect of Oncomutations and Posttranslational Modifications of Histone H1 on Chromatosome Structure and Stability Moscow University Biological Sciences Bulletin. 74: 121-126. DOI: 10.3103/S0096392519030015  0.574
2019 Novoseletsky V, Lozhnikov M, Armeev G, Kudriavtsev A, Shaytan A, Kobelkov G, Shaitan K. Abstract P-49: Determination of Relative Positions of Two Helices in Two-Helical Proteins Basing on X-ray Diffraction Data with the Use of Convolutional Neural Networks International Journal of Biomedicine. 9. DOI: 10.21103/Ijbm.9.Suppl_1.P49  0.512
2019 Lozhnikov M, Kobelkov G, Armeev G, Kudriavtsev A, Novoseletsky V, Shaytan A, Shaitan K. Abstract P-47: Recognition of Single Particle’s Diffraction Images Generated in X-ray Free Electron Laser Experiments International Journal of Biomedicine. 9. DOI: 10.21103/Ijbm.9.Suppl_1.P47  0.492
2019 Armeev G, Lozhnikov M, Novoseletsky V, Kudriavtsev A, Shaytan A, Kobelkov G, Shaitan K. Abstract P-43: Approximating Protein Alpha-Helices with Cylinders for Free Electron Lasers Diffraction Experiments International Journal of Biomedicine. 9. DOI: 10.21103/Ijbm.9.Suppl_1.P43  0.508
2019 Bass M, Armeev G, Shaytan A. Abstract P-20: Linker Histone H1: The Interplay between Chromatosome Stability, Oncomutations and Post-Translational Modifications International Journal of Biomedicine. 9. DOI: 10.21103/Ijbm.9.Suppl_1.P20  0.384
2019 Armeev G, Panchenko A, Shaytan A. Abstract OR-19: Integrative Approach on Nucleosome Complexes Modeling International Journal of Biomedicine. 9. DOI: 10.21103/Ijbm.9.Suppl_1.Or19  0.572
2018 Shaytan AK, Xiao H, Armeev GA, Gaykalova DA, Komarova GA, Wu C, Studitsky VM, Landsman D, Panchenko AR. Structural interpretation of DNA-protein hydroxyl-radical footprinting experiments with high resolution using HYDROID. Nature Protocols. PMID 30341436 DOI: 10.1038/S41596-018-0048-Z  0.589
2018 Gorkovets TK, Armeev GA, Shaitan KV, Shaytan AK. Joint Effect of Histone H1 Amino Acid Sequence and DNA Nucleotide Sequence on the Structure of Chromatosomes: Analysis by Molecular Modeling Methods Moscow University Biological Sciences Bulletin. 73: 82-87. DOI: 10.3103/S0096392518020025  0.566
2017 Xiao H, Wang F, Wisniewski J, Shaytan AK, Ghirlando R, FitzGerald PC, Huang Y, Wei D, Li S, Landsman D, Panchenko AR, Wu C. Molecular basis of CENP-C association with the CENP-A nucleosome at yeast centromeres. Genes & Development. PMID 29074736 DOI: 10.1101/Gad.304782.117  0.662
2017 Shaytan AK, Xiao H, Armeev GA, Wu C, Landsman D, Panchenko AR. Hydroxyl-radical footprinting combined with molecular modeling identifies unique features of DNA conformation and nucleosome positioning. Nucleic Acids Research. 45: 9229-9243. PMID 28934480 DOI: 10.1093/Nar/Gkx616  0.638
2017 El Kennani S, Adrait A, Shaytan AK, Khochbin S, Bruley C, Panchenko AR, Landsman D, Pflieger D, Govin J. MS_HistoneDB, a manually curated resource for proteomic analysis of human and mouse histones. Epigenetics & Chromatin. 10: 2. PMID 28096900 DOI: 10.1186/S13072-016-0109-X  0.623
2017 Gribkova AK, Armeev GA, Shaytan AK. Investigation of histone-DNA binding energy as a function of DNA unwrapping from nucleosome using molecular modeling Moscow University Biological Sciences Bulletin. 72: 142-145. DOI: 10.3103/S009639251703004X  0.37
2016 Biswas R, Gao S, Cultraro CM, Maity TK, Venugopalan A, Abdullaev Z, Shaytan AK, Carter CA, Thomas A, Rajan A, Song Y, Pitts S, Chen K, Bass S, Boland J, et al. Genomic profiling of multiple sequentially acquired tumor metastatic sites from an "exceptional responder" lung adenocarcinoma patient reveals extensive genomic heterogeneity and novel somatic variants driving treatment response. Cold Spring Harbor Molecular Case Studies. 2: a001263. PMID 27900369 DOI: 10.1101/mcs.a001263  0.51
2016 Valieva ME, Armeev GA, Kudryashova KS, Gerasimova NS, Shaytan AK, Kulaeva OI, McCullough LL, Formosa T, Georgiev PG, Kirpichnikov MP, Studitsky VM, Feofanov AV. Large-scale ATP-independent nucleosome unfolding by a histone chaperone. Nature Structural & Molecular Biology. PMID 27820806 DOI: 10.1038/Nsmb.3321  0.439
2016 Studitsky VM, Nizovtseva EV, Shaytan AK, Luse DS. Nucleosomal Barrier to Transcription: Structural Determinants and Changes in Chromatin Structure. Biochemistry & Molecular Biology Journal. 2. PMID 27754494 DOI: 10.21767/2471-8084.100017  0.406
2016 Shaytan AK, Armeev GA, Goncearenco A, Zhurkin VB, Landsman D, Panchenko AR. Trajectories of microsecond molecular dynamics simulations of nucleosomes and nucleosome core particles. Data in Brief. 7: 1678-81. PMID 27222871 DOI: 10.1016/J.Dib.2016.04.073  0.755
2016 Draizen EJ, Shaytan AK, Mariño-Ramírez L, Talbert PB, Landsman D, Panchenko AR. HistoneDB 2.0: a histone database with variants--an integrated resource to explore histones and their variants. Database : the Journal of Biological Databases and Curation. 2016. PMID 26989147 DOI: 10.1093/Database/Baw014  0.652
2016 Armeev GA, Shaitan KV, Shaytan AK. Nucleosome structure relaxation during DNA unwrapping: Molecular dynamics simulation study Moscow University Biological Sciences Bulletin. 71: 141-144. DOI: 10.3103/S0096392516030020  0.616
2016 Armeev GA, Gorkovets TK, Efimova DA, Shaitan KV, Shaytan AK. Modeling of the structure of protein–DNA complexes using the data from FRET and footprinting experiments Moscow University Biological Sciences Bulletin. 71: 29-33. DOI: 10.3103/S0096392516010016  0.473
2016 Shaitan KV, Armeev GA, Shaytan AK. The dynamics of irreversible evaporation of a water–protein droplet and the problem of structural and dynamic experiments with single molecules Biophysics. 61: 177-184. DOI: 10.1134/S0006350916020172  0.5
2016 Lyubitelev AV, Nikitin DV, Shaytan AK, Studitsky VM, Kirpichnikov MP. Structure and functions of linker histones Biochemistry (Moscow). 81: 213-223. DOI: 10.1134/S0006297916030032  0.418
2016 Draizen EJ, Shaytan AK, Mariño-Ramírez L, Talbert PB, Landsman D, Panchenko AR. HistoneDB 2.0: A histone database with variants - An integrated resource to explore histones and their variants Database. 2016. DOI: 10.1093/database/baw014  0.654
2016 Shaytan AK, Armeev GA, Goncearenco A, Zhurkin VB, Landsman D, Panchenko AR. Trajectories of microsecond molecular dynamics simulations of nucleosomes and nucleosome core particles Data in Brief. 7: 1678-1681. DOI: 10.1016/j.dib.2016.04.073  0.755
2016 Shaytan AK, Armeev GA, Goncearenco A, Zhurkin VB, Landsman D, Panchenko AR. Nucleosome Dynamics at Microsecond Timescale: DNA-Protein Interactions, Water-Mediated Interactions and Nucleosome Formation Biophysical Journal. 110: 405. DOI: 10.1016/J.Bpj.2015.11.2189  0.804
2015 Shaytan AK, Armeev GA, Goncearenco A, Zhurkin VB, Landsman D, Panchenko AR. Coupling between histone conformations and DNA geometry in nucleosomes on a microsecond timescale: atomistic insights into nucleosome functions. Journal of Molecular Biology. PMID 26699921 DOI: 10.1016/J.Jmb.2015.12.004  0.802
2015 Gaykalova DA, Kulaeva OI, Volokh O, Shaytan AK, Hsieh FK, Kirpichnikov MP, Sokolova OS, Studitsky VM. Structural analysis of nucleosomal barrier to transcription. Proceedings of the National Academy of Sciences of the United States of America. 112: E5787-95. PMID 26460019 DOI: 10.1073/Pnas.1508371112  0.404
2015 Goncearenco A, Shaytan AK, Shoemaker BA, Panchenko AR. Structural Perspectives on the Evolutionary Expansion of Unique Protein-Protein Binding Sites. Biophysical Journal. 109: 1295-306. PMID 26213149 DOI: 10.1016/J.Bpj.2015.06.056  0.706
2015 Shaytan AK, Armeev GA, Goncearenco A, Zhurkin VB, Landsman D, Panchenko AR. 6 Combined influence of linker DNA and histone tails on nucleosome dynamics as revealed by microsecond molecular dynamics simulations. Journal of Biomolecular Structure & Dynamics. 33: 3. PMID 26103217 DOI: 10.1080/07391102.2015.1032630  0.784
2015 Shaytan AK, Landsman D, Panchenko AR. Nucleosome adaptability conferred by sequence and structural variations in histone H2A-H2B dimers. Current Opinion in Structural Biology. 32: 48-57. PMID 25731851 DOI: 10.1016/J.Sbi.2015.02.004  0.667
2015 Armeev GA, Shaitan KV, Shaytan AK. Conformational flexibility of nucleosomes: A molecular dynamics study Moscow University Biological Sciences Bulletin. 70: 147-151. DOI: 10.3103/S0096392515030025  0.561
2015 Shaytan AK, Armeev GA, Zhurkin VB, Landsman D, Panchenko AR. Polymorphism of Histone Tail Interactions in Nucleosome Biophysical Journal. 108. DOI: 10.1016/J.Bpj.2014.11.431  0.704
2014 Nishi H, Shaytan A, Panchenko AR. Physicochemical mechanisms of protein regulation by phosphorylation. Frontiers in Genetics. 5: 270. PMID 25147561 DOI: 10.3389/Fgene.2014.00270  0.736
2014 Bozdaganyan ME, Orekhov PS, Shaytan AK, Shaitan KV. Comparative computational study of interaction of C60-fullerene and tris-malonyl-C60-fullerene isomers with lipid bilayer: relation to their antioxidant effect. Plos One. 9: e102487. PMID 25019215 DOI: 10.1371/journal.pone.0102487  0.465
2014 Kasimova MA, Tarek M, Shaytan AK, Shaitan KV, Delemotte L. Voltage-gated ion channel modulation by lipids: insights from molecular dynamics simulations. Biochimica Et Biophysica Acta. 1838: 1322-31. PMID 24513257 DOI: 10.1016/J.Bbamem.2014.01.024  0.473
2014 Chang HW, Kulaeva OI, Shaytan AK, Kibanov M, Kuznedelov K, Severinov KV, Kirpichnikov MP, Clark DJ, Studitsky VM. Analysis of the mechanism of nucleosome survival during transcription. Nucleic Acids Research. 42: 1619-27. PMID 24234452 DOI: 10.1093/Nar/Gkt1120  0.331
2014 Kasimova M, Shaytan A, Shaitan K, Tarek M. Investigation of Ion Permeation through the Cx26 Hemichannel Biophysical Journal. 106: 5-6. DOI: 10.1016/J.Bpj.2013.11.3093  0.517
2014 Kasimova M, Delemotte L, Polak A, Miklavcic D, Casciola M, Apollonio F, Breton M, Mir L, Shaytan A, Shaitan K, Tarek M. Molecular Insights into Electroporation and Electrotransfer through Model Cell Membranes Biophysical Journal. 106: 291. DOI: 10.1016/J.Bpj.2013.11.1701  0.533
2013 Chang H, Kulaeva OI, Shaytan A, Kibanov M, Severinov K, Clark DJ, Studitsky VM. Pausing as a mechanism of nucleosome recovery Epigenetics & Chromatin. 6. DOI: 10.1186/1756-8935-6-S1-P14  0.398
2012 Orekhov PS, Shaytan AK, Shaitan KV. Calculation of spectral shifts of the mutants of bacteriorhodopsin by QM/MM methods Biophysics. 57: 144-152. DOI: 10.1134/S0006350912020170  0.424
2010 Shaytan AK, Ivanov VA, Shaitan KV, Khokhlov AR. Free energy profiles of amino acid side chain analogs near water-vapor interface obtained via MD simulations. Journal of Computational Chemistry. 31: 204-16. PMID 19421988 DOI: 10.1002/Jcc.21267  0.477
2009 Shaytan AK, Shaitan KV, Khokhlov AR. Solvent accessible surface area of amino acid residues in globular proteins: correlation of apparent transfer free energies with experimental hydrophobicity scales. Biomacromolecules. 10: 1224-37. PMID 19334678 DOI: 10.1021/Bm8015169  0.482
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