Marta Kulik

e-mail: m.kulik /at/ uw.edu.pl address: Biological and Chemical Research Centre Żwirki i Wigury 101 02-089 Warsaw, Poland room: 4.116 Researchgate orcid.org/0000-0003-2381-7665 ResearcherID Google Scholar

Publications

Wlodawer, A., Rubach, P., Dauter, Z., Dec, W., Brzezinski, D., Kulik, M., Minor, W., & Jaskolski, M. (2026). Comparative assessment of crystallographic and cryo‐ EM models in the Protein Data Bank. FEBS Open Bio. https://doi.org/10.1002/2211-5463.70326
Rybicka, P. M., Kulik, M., Ignat’ev, V., & Dominiak, P. M. (2026). From atoms to a data bank: optimizing transferability of electron-density symmetry. Acta Crystallographica Section A Foundations and Advances, 82(4), 256-275. https://doi.org/10.1107/s2053273326004651
Femoen, V. J., Pacoste, L., Chodkiewicz, M. L., Afonine, P. V., Poon, B. K., Kulik, M., Golon, Ł., Moriarty, N. W., Adams, P. D., Hofer, G., Dominiak, P. M., Liebschner, D., & Zou, X. (2026). pyDiSCaMB  : enabling the use of multipolar scattering factors in Phenix. Journal of Applied Crystallography, 59(2), 662–672. https://doi.org/10.1107/s1600576726000828
Kulik, M., & Dominiak, P. M. (2025). Protein electrostatic potential Fourier maps calculated using the transferable aspherical atom model and the independent atom model across resolutions IUCrJ, 12, 616-632. https://doi.org/10.1107/S2052252525008383
Chyży, P., Kulik, M., Shinobu, A., Re, S., Sugita, Y., & Trylska, J. (2024). Molecular dynamics in multidimensional space explains how mutations affect the association path of neomycin to a riboswitch. Proceedings of the National Academy of Sciences, 121(15). https://doi.org/10.1073/pnas.2317197121
Budniak, U. A., Karolak, N. K., Kulik, M., Młynarczyk, K., Górna, M. W., & Dominiak, P. M. (2022). The Role of Electrostatic Interactions in IFIT5-RNA Complexes Predicted by the UBDB+EPMM Method. The Journal of Physical Chemistry B, 126(45), 9152–9167. https://doi.org/10.1021/acs.jpcb.2c04519
Kulik, M., & Dominiak, P. M. (2022). Electron density is not spherical: the many applications of the transferable aspherical atom model. Computational and Structural Biotechnology Journal, 20, 6237–6243. https://doi.org/10.1016/j.csbj.2022.10.018
Rybicka, P. M., Kulik, M., Chodkiewicz, M. L., & Dominiak, P. M. (2022). Multipolar Atom Types from Theory and Statistical Clustering (MATTS) Data Bank: Impact of Surrounding Atoms on Electron Density from Cluster Analysis. Journal of Chemical Information and Modeling, 62(16), 3766–3783. https://doi.org/10.1021/acs.jcim.2c00145
Kulik, M., Chodkiewicz, M. L., & Dominiak, P. M. (2022). Theoretical 3D electron diffraction electrostatic potential maps of proteins modeled with a multipolar pseudoatom data bank. Acta Crystallographica Section D Structural Biology, 78(8), 1010–1020. https://doi.org/10.1107/s2059798322005836
Nishima, W., & Kulik, M. (2021). Full-Length Computational Model of the SARS-CoV-2 Spike Protein and Its Implications for a Viral Membrane Fusion Mechanism. Viruses, 13(6), 1126. https://doi.org/10.3390/v13061126
Chyży, P., Kulik, M., Re, S., Sugita, Y., & Trylska, J. (2021). Mutations of N1 Riboswitch Affect its Dynamics and Recognition by Neomycin Through Conformational Selection. Frontiers in Molecular Biosciences, 8, 633130. https://doi.org/10.3389/fmolb.2021.633130
Kulik, M., Mori, T., & Sugita, Y. (2021). Multi-Scale Flexible Fitting of Proteins to Cryo-EM Density Maps at Medium Resolution. Frontiers in Molecular Biosciences, 8, 631854. https://doi.org/10.3389/fmolb.2021.631854
Brunner, J. S., Vogel, A., Lercher, A., Caldera, M., Korosec, A., Pühringer, M., Hofmann, M., Hajto, A., Kieler, M., Garrido, L. Q., Kerndl, M., Kuttke, M., Mesteri, I., Górna, M. W., Kulik, M., Dominiak, P. M., Brandon, A. E., Estevez, E., Egan, C. L., … Schabbauer, G. (2020). The PI3K pathway preserves metabolic health through MARCO-dependent lipid uptake by adipose tissue macrophages. Nature Metabolism, 2(12), 1427–1442. https://doi.org/10.1038/s42255-020-00311-5
Mori, T., Kulik, M., Miyashita, O., Jung, J., Tama, F., & Sugita, Y. (2019). Acceleration of cryo-EM Flexible Fitting for Large Biomolecular Systems by Efficient Space Partitioning. Structure, 27(1), 161-174.e3. https://doi.org/10.1016/j.str.2018.09.004
Kulik, M., Mori, T., Sugita, Y., & Trylska, J. (2018). Molecular mechanisms for dynamic regulation of N1 riboswitch by aminoglycosides. Nucleic Acids Research, 46 (19), 9960-9970. https://doi.org/10.1093/nar/gky833
Jasiński, M., Kulik, M., Wojciechowska, M., Stolarski, R., & Trylska, J. (2018). Interactions of 2’-O-methyl oligoribonucleotides with the RNA models of the 30S subunit A-site. PLOS ONE, 13(1), e0191138. https://doi.org/10.1371/journal.pone.0191138
Kulik, M., Markowska-Zagrajek, A., Wojciechowska, M., Grzela, R., Wituła, T., & Trylska, J. (2017). Helix 69 of Escherichia coli 23S ribosomal RNA as a peptide nucleic acid target. Biochimie, 138, 32–42. https://doi.org/10.1016/j.biochi.2017.04.001
Trylska, J., & Kulik, M. (2016). Interactions of aminoglycoside antibiotics with rRNA. Biochemical Society Transactions, 44(4), 987–993. https://doi.org/10.1042/bst20160087
Kulik, M., Goral, A. M., Jasiński, M., Dominiak, P. M., & Trylska, J. (2015). Electrostatic Interactions in Aminoglycoside-RNA Complexes. Biophysical Journal, 108(3), 655–665. https://doi.org/10.1016/j.bpj.2014.12.020
Kulik, M., & Trylska, J. (2016). Structural and energetic comparison of the complexes of aminoglycosides with the model of the ribosomal A-site. RAIRO – Operations Research, 50(2), 375–386. https://doi.org/10.1051/ro/2015041
Kulik, M., Pazio, A., & Wozniak, K. (2013). Bis(L-serinium) oxalate dihydrate: polymorph II. Acta Crystallographica Section E Structure Reports Online, 69(11), o1667–o1668. https://doi.org/10.1107/s160053681302727x