Tags: Skrynnikov, Vologda
Posts tagged ‘Skrynnikov’
X-ray Crystallography Module in MD Simulation Program Amber 2023. Refining the Models of Protein Crystals
Posted: 26.12.2023
Here, we present the new crystallography module xray, released as a part of the Amber 2023 package.
Oleg Mikhailovskii, Sergei A. Izmailov, Yi Xue, David A. Case, and Nikolai R. Skrynnikov
https://pubs.acs.org/doi/10.1021/acs.jcim.3c01531
(more…)Tags: Izmailov, Mikhailovskii, Skrynnikov
Using NMR diffusion data to validate MD models of disordered proteins: Test case of N-terminal tail of histone H4
Posted: 20.11.2023
Here, we investigate, both experimentally and via the MD modeling, the translational diffusion of a 25-residue N-terminal fragment from histone H4 (N-H4).
Olga O Lebedenko, Vladislav A Salikov, Sergei A Izmailov, Ivan S Podkorytov, Nikolai R Skrynnikov
https://www.sciencedirect.com/science/article/abs/pii/S0006349523007208
(more…)Tags: Izmailov, Podkorytov, Salikov, Skrynnikov
Conformational and Interaction Landscape of Histone H4 Tails in Nucleosomes Probed by Paramagnetic NMR Spectroscopy
Posted: 09.11.2023
Wenjun Sun, Olga O. Lebedenko, Nicole Gonzalez Salguero, Matthew D. Shannon, Mohamad Zandian, Michael G. Poirier, Nikolai R. Skrynnikov, and Christopher P. Jaroniec
https://pubs.acs.org/doi/full/10.1021/jacs.3c10340
(more…)Tags: Lebedenko, Skrynnikov
Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD
Posted: 12.01.2023
Diego F. Gauto, Olga O. Lebedenko, Lea Marie Becker, Isabel Ayala, Roman Lichtenecker, Nikolai R. Skrynnikov, Paul Schanda
https://www.sciencedirect.com/science/article/pii/S2590152422000204?via%3Dihub
(more…)Tags: Lebedenko, Skrynnikov
Simulating diffraction photographs based on molecular dynamics trajectories of a protein crystal: a new option to examine structure-solving strategies in protein crystallography
Posted: 11.01.2023
Ning Liu, Oleg Mikhailovskii, Nikolai R. Skrynnikovb, and Yi Xue
https://journals.iucr.org/m/issues/2023/01/00/lz5062/index.html
(more…)Tags: Mikhailovskii, Ning Liu, Skrynnikov, Yi Xue
Effect of rotation in NMR diffusion experiments on micron-sized particles: A generalized theoretical treatment
Posted: 17.11.2022
Ivan S.Podkorytov, Nikolai R.Skrynnikov
https://doi.org/10.1016/j.jmr.2022.107303
(more…)
Tags: Podkorytov, Skrynnikov
Amber22 is now available!
Posted: 27.04.2022
D.A. Case, H.M. Aktulga, K. Belfon, I.Y. Ben-Shalom, J.T. Berryman, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, G.A. Cisneros, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, G. Giambasu, M.K. Gilson, H. Gohlke, A.W. Goetz, R. Harris, S. Izadi, S.A. Izmailov, K. Kasavajhala, M.C. Kaymak, E. King, A. Kovalenko, T. Kurtzman, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, M. Machado, V. Man, M. Manathunga, K.M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, H. Nguyen, K.A. O’Hearn, A. Onufriev, F. Pan, S. Pantano, R. Qi, A. Rahnamoun, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, A. Shajan, J. Shen, C.L. Simmerling, N.R. Skrynnikov, J. Smith, J. Swails, R.C. Walker, J. Wang, J. Wang, H. Wei, R.M. Wolf, X. Wu, Y. Xiong, Y. Xue, D.M. York, S. Zhao, and P.A. Kollman
https://ambermd.org/doc12/Amber22.pdf
(more…)Tags: Izmailov, Mikhailovskii, Skrynnikov, Yi Xue
Modeling a unit cell: crystallographic refinement procedure using the biomolecular MD simulation platform Amber
Posted: 23.12.2021
Oleg Mikhailovskii, Yi Xue, and Nikolai R. Skrynnikov.
https://doi.org/10.1107/S2052252521011891.
(more…)Tags: Mikhailovskii, Skrynnikov
The Role of Rotational Motion in Diffusion NMR Experiments on Supramolecular Assemblies: Application to Sup35NM Fibrils
Posted: 23.04.2021
Dr. Boris B. Kharkov, Ivan S. Podkorytov, Dr. Stanislav A. Bondarev, Dr. Mikhail V. Belousov, Vladislav A. Salikov, Prof. Dr. Galina A. Zhouravleva, Prof. Dr. Nikolai R. Skrynnikov
https://doi.org/10.1002/anie.202102408
(more…)Tags: Kharkov, Podkorytov, Salikov, Skrynnikov