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Том 20   Выпуск 2   Год 2025
Список литературы

  1. Brown P.J., Fox A.G., Maslen E.N., O’Keefe M.A., Willis B.T.M. Intensity of diffracted intensities. In: International Tables for Crystallography. Ed. E. Prince. 2006. Vol. C. P. 554–595. doi: 10.1107/97809553602060000600
  2. Peng L.-M. Electron atomic scattering factors and scattering potentials of crystals. Micron. 1999;30:625–648. doi: 10.1016/S0968-4328(99)00033-5
  3. Doyle P.A., Turner P.S. Relativistic Hartree–Fock X-ray and electron scattering factors. Acta Cryst. 1968;A24:390–397. doi: 10.1107/S0567739468000756
  4. Diamond R. A real-space refinement procedure for proteins. Acta Cryst. 1971;A27:436-452. doi: 10.1107/S0567739471000986
  5. Rupp B. Biomolecular Crystallography. Principles, Practice, and Applications to Structural Biology. New York (USA): Garland Science, Taylor & Francis Group, 2009.
  6. Urzhumtsev A.G., Lunin V.Y. Introduction to crystallographic refinement of macromolecular atomic models. Crystallography Reviews. 2019;25(3):164-262. doi: 10.1080/0889311X.2019.1631817
  7. Lunin V.Y., Lunina N.L. The separation of the effects of atomic displacement and local resolution in crystallographic and cryo-electron microscopy maps. Acta Cryst. 2025;A81(6). doi: 10.1107/S2053273325008034
  8. Cardone G., Heymann J.B., Steven A.C. One number does not fit all: Mapping local variations in resolution in cryo-EM reconstructions. J. Struct. Biol. 2013;184:226–236. doi: 10.1016/j.jsb.2013.08.002
  9. Kucukelbir A., Sigworth F.J., Tagare H.D. Quantifying the local resolution of cryo-EM density maps. Nat. Methods. 2014;11:63–65. doi: 10.1038/nmeth.2727
  10. Vilas J.L., Gómez-Blanco J., Conesa P., Melero R., de la Rosa-Trevín J.M., Otón J., Cuenca J., Marabini R., Carazo J.M., Vargas J., Sorzano C.O.S. MonoRes: Automatic and Accurate Estimation of Local Resolution for Electron Microscopy Maps. Structure. 2018;26:337–344. doi: 10.1016/j.str.2017.12.018
  11. Urzhumtsev A., Lunin V.Y. Analytic modeling of inhomogeneous-resolution maps in cryo electron microscopy and crystallography. IUCrJ. 2022;9:728–734. doi: 10.1107/S2052252522008260
  12. Żyła D.S., Wiegand T., Bachmann P., Zdanowicz R., Giese C., Meier B.H., Waksman G., Hospen-thal M.K., Glockshuber R. The assembly platform FimD is required to obtain the most stable qua-ternary structure of type 1 pili. Nat. Commun. 2024;15:3032. doi: 10.1038/s41467-024-47212-9
  13. Kawahara K., Oki H., Iimori M., Muramoto R., Imai T., Gerle C., Shigematsu H., Matsuda S., Iida T., Nakamura S. High-resolution cryo-EM analysis visualizes hydrated type I and IV pilus struc-tures from enterotoxigenic Escherichia coli. Structure. 2025;33(6):1040–1050. doi: 10.1016/j.str.2025.03.010
  14. Petrova T.E., Glukhov A.S., Stetsenko A., Guskov A., Gabdulkhakov A.G. Determination of the water network surrounding the type I pilus from E. coli by cryo-electron microscopy. bioRxiv. 2025. doi: 10.1101/2025.09.07.674696
  15. Penczek P.A. Chapter Three - Resolution Measures in Molecular Electron Microscopy. Methods Enzymol. 2010;482:73–100. doi: 10.1016/S0076-6879(10)82003-8
  16. Urzhumtseva L., Klaholz B., Urzhumtsev A. On effective and optical resolutions of diffraction data sets. Acta Cryst. 2013;D69:1921–1934. doi: 10.1107/S0907444913016673
  17. Saxton W.O., Baumeister W. The correlation averaging of a regularly arranged bacterial cell envelope protein. J. Microsc. 1982;127:127−138. doi: 10.1111/j.1365-2818.1982.tb00405.x
  18. Harauz G., van Heel M. Exact filters for general geometry three dimensional reconstruction. Optik. 1986;73:146−156.
  19. Van Heel M. Similarity measures between images. Ultramicroscopy. 1978;21:95–100. doi: 10.1016/0304-3991(87)90010-6
  20. Urzhumtsev A. Straightening FSC curves. bioRxiv. 2025. doi: 10.1101/2025.06.22.660909
  21. Lunin V.Y., Lunina N.L., Urzhumtsev A.G. Local heterogeneity analysis of crystallographic and cryo-EM maps using shell-approximation. Current Research in Structural Biology. 2023;6:100102. doi: 10.1016/j.crstbi.2023.100102
  22. Urzhumtsev A.G., Lunin V.Y. Gaussian-convolution-invariant shell approximation to spherically-symmetric functions. arXiv: 2412.14350. 2024. doi: 10.48550/arXiv.2412.14350
  23. Adams P.D., Afonine P.V., Bunkóczi G., Chen V.B., Davis I.W., Echols N., Headd J.J., Hung L.W., Kapral G.J., Grosse-Kunstleve R.W., et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Cryst. 2010;D66:213−221. doi: 10.1107/S0907444909052925
  24. Afonine P.V., Poon B.K., Read R.J., Sobolev O.V., Terwilliger T.C., Urzhumtsev A., Adams P.D. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. 2018;D74:531–544. doi: 10.1107/S2059798318006551
  25. Terwilliger T.C., Sobolev O.V., Afonine P.V., Adams P.D. Automated map sharpening by maximization of detail and connectivity. Acta Cryst. 2018;D74:545–559. doi: 10.1107/S2059798318004655
Содержание
Оригинальная статья
Лунин В.Ю., Лунина Н.Л., Петрова Т.Е. Оценка локальной неоднородности крио-ЭМ карт в прямом пространстве для пилей типа I из E. coli. Математическая биология и биоинформатика. 2025;20(2):509-519. doi: 10.17537/2025.20.509
(опубликована на рус. яз.)

Аннотация (рус.)
Аннотация (англ.)
Полный текст (рус., pdf)
Список литературы
Перевод на англ. яз.

Lunin V.Y., Lunina N.L., Petrova T.E. Estimation of Local Heterogeneity of Cryo-EM Maps in Direct Space for Type I Pilus from E. coli . Маthematical biology and bioinformatics. 2026, 21(Suppl.):t1-t10. doi: 10.17537/2026.21.t1

Полный текст (англ., pdf)

 
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