Список литературы
- Páll S., Zhmurov A., Bauer P., Abraham M., Lundborg M., Gray A., Lundborg M., Gray A., Hess B., Lindahl E. Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACS. J. Chem. Phys. 2020;153(13):134110. doi: 10.1063/5.0018516
- Fedorov V.A., Kholina E.G., Kovalenko I.B., Gudimchuk N.B. Performance analysis of different computational architectures: Molecular dynamics in application to protein assemblies, illustrated by microtubule and electron transfer proteins. Supercomput. Front. Innov. 2018;5(4):11–114. doi: 10.14529/jsfi180414
- Fedorov V.A., Kholina E.G., Kovalenko I.B., Gudimchuk N.B., Orekhov P.S., Zhmurov A.A. Update on Performance Analysis of Different Computational Architectures: Molecular Dynamics in Application to Protein-Protein Interactions. Supercomput. Front. Innov. 2020;7(4):62–67. doi: 10.14529/jsfi200405
- Kavallaris M. Microtubules and resistance to tubulin-binding agents. Nat. Rev. Cancer. 2010;10(3):194–204. doi: 10.1038/nrc2803
- Jordan M.A., Wilson L. Microtubules as a target for anticancer drugs. Nat. Rev. Cancer. 2004;4(4):253–265. doi: 10.1038/nrc1317
- Fedorov V.A., Orekhov P.S., Kholina E.G., Zhmurov A.A., Ataullakhanov F.I., Kovalenko I.B., Gudimchuk N.B. Mechanical properties of tubulin intra- and inter-dimer interfaces and their implications for microtubule dynamic instability. PLoS Comput. Biol. 2019;15(8):e1007327. doi: 10.1371/journal.pcbi.1007327
- Alushin G.M., Lander G.C., Kellogg E.H., Zhang R., Baker D., Nogales E. High-resolution microtubule structures reveal the structural transitions in αβ-tubulin upon GTP hydrolysis. Cell. 2014;157(5):1117–1129. doi: 10.1016/j.cell.2014.03.053
- Webb B., Sali A. Comparative protein structure modeling using MODELLER. Curr. Protoc. Bioinformatics. 2016;54(1):5–6. doi: 10.1002/cpbi.3
- Olsson M.H.M., Søndergaard C.R., Rostkowski M., Jensen J.H. PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions. J. Chem. Theory Comput. 2011;7(2):525–537. doi: 10.1021/ct100578z
- Morozenko A., Stuchebrukhov A.A. Dowser++, a new method of hydrating protein structures. Proteins. 2016;84(10):1347–1357. doi: 10.1002/prot.25081
- MacKerell A.D., Bashford D., Bellott M., Dunbrack R.L., Evanseck J.D., Field M.J., Fischer S., Gao J., Guo H., Ha S., Joseph-McCarthy D. et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 1998;102(18):3586–3616. doi: 10.1021/jp973084f
- MacKerell A.D. Jr., Feig M., Brooks C.L. Improved treatment of the protein backbone in empirical force fields. J. Am. Chem. Soc. 2004;126(3):698–699. doi: 10.1021/ja036959e
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