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
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
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
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
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
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
Boris 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
Sevastyan Rabdano and Sergei Izmailov took part in the FEBS Congress on July 7-12, 2018 in Prague.
Sevastyan Rabdano presented the poster “ESR spectroscopy as a probe of protein dynamics: the effect of different motional modes on the simulated lineshapes”.
Sergei Izmailov presented the poster “ESR spectroscopy as a probe of protein dynamics: an insight from long MD simulations”.
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
Rogacheva, O. N.; Izmailov, S. A.; Slipchenko, L. V.; Skrynnikov, N. R. A New Structural Arrangement in Proteins Involving Lysine NH3 + Group and Carbonyl. Scientific Reports 2017, 7 (1).
DOI: 10.1038/s41598-017-16584-y.
Tags: Izmailov, Rogacheva, Skrynnikov
