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
Posts tagged ‘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: 11.01.2023Effect 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
Histone H4 tails in nucleosomes: a fuzzy interaction with DNA
Posted: 24.02.2021
Sevastyan O. Rabdano, Matthew D. Shannon, Sergei A. Izmailov, Nicole Gonzalez Salguero, Mohamad Zandian, Rudra N. Purusottam, Michael G. Poirier, Nikolai R. Skrynnikov and Christopher P. Jaroniec
https://doi.org/10.1002/anie.202012046
(more…)Tags: Izmailov, Rabdano, Skrynnikov
Structural and dynamic origins of ESR lineshapes in spin-labeled GB1 domain: the insights from spin dynamics simulations based on long MD trajectories
Posted: 20.01.2020
Izmailov, S.A, Rabdano, S.O., Hasanbasri, Z., Podkorytov, I.S., Saxena, S., Skrynnikov, N.R. Structural and dynamic origins of ESR lineshapes in spin-labeled GB1 domain: the insights from spin dynamics simulations based on long MD trajectories. Scientific Reports 2020.
DOI: 10.1038/s41598-019-56750-y
Tags: Izmailov, Podkorytov, Rabdano, Skrynnikov
Molecular Dynamics model of peptide-protein conjugation: case study of covalent complex between Sos1 peptide and N-terminal SH3 domain from Grb2
Posted: 26.12.2019
Luzik, D.A., Rogacheva, O.N., Izmailov, S.A., Indeykina, M.I., Kononikhin, A.S., Skrynnikov, N.R. Molecular Dynamics model of peptide-protein conjugation: case study of covalent complex between Sos1 peptide and N-terminal SH3 domain from Grb2. Scientific Reports 2019.
DOI:
Tags: Izmailov, Luzik, Rogacheva, Skrynnikov
4-th annual meeting of Institute of Translational Biomedicine of SPbSU, Saint Petersburg, Russia
Posted: 20.07.2018Boris Kharkov, Sergey Izmailov, Sevastyan Rabdano, Nikolai Skrynnikov, Dmitry Luzik, Olga Rogacheva and Ivan Podkorytov took part in the fourth annual conference of the Institute of Translational Biomedicine, which was held on July 20-22, 2018 in St. Petersburg.
Sergei Izmailov presented the report “EPR tags as a probe for studying protein systems: what the spectra say.”
Ivan Podkorytov presented the report “Research of mobile Sup35NM protein sites in monomers and in the composition of fibrils by NMR with diffusion filter”.
Olga Rogacheva presented the report “Bioconjugation of peptides in the context of targeted therapy: modeling and experiment.”
Dmitry Luzik presented the report “Covalent binding of modified Sos1-derived peptide and N-terminal SH3-domain of adapter protein Grb2”.
Sevastyan Rabdano presented the report “ESR spectroscopy as a probe of protein dynamics: an insight from long MD simulations”.
Tags: Izmailov, Kharkov, Luzik, Podkorytov, Rabdano, Rogacheva, Skrynnikov
15-th International School-Conference Magnetic resonance and its applications Spinus 2018
Posted: 01.04.2018
Sergey Izmailov, Sevastyan Rabdano, Nikolai Skrynnikov, Boris Kharkov and Vladislav Salikov took part in the 15th international school-conference “Magnetic Resonance and Its Applications, Spinus” held on April 1-6, 2018.
Sergey Izmailov presented the report “EPR spectra simulation from MD data using Redfield theory and direct propagation method”.
Sevastyan Rabdano presented the report “Dynamic modes in spin-labeled protein revealed by MD simulations: experimental and computed EPR spectra”.
Nikolai Skrynnikov presented the lecture “Many faces of disulfide bond”.
Boris Kharkov presented the report “Skin-Effect Compensated Optimal Control Pulses for Excitation in a Conductive Medium”.
Vladislav Salikov presented the poster “Optimization of bacterial expression of MdmX N-terminal domain for NMR studies”.
Tags: Izmailov, Kharkov, Rabdano, Salikov, Skrynnikov