Search results
- 1.0583721 - BFÚ 2024 RIV NL eng J - Journal Article
Luo, Y. - Granzhan, A. - Marquevielle, J. - Cucchiarini, A. - Lacroix, L. - Amrane, S. - Verga, D. - Mergny, Jean-Louis
Guidelines for G-quadruplexes: I. In vitro characterization.
Biochimie. Roč. 214, NOV 2023 (2023), s. 5-23. ISSN 0300-9084. E-ISSN 1638-6183
R&D Projects: GA MŠMT EF15_003/0000477
Institutional support: RVO:68081707
Keywords : resonance energy-transfer * single-stranded-dna * rna g-quadruplexes * circular-dichroism * nucleic-acids * thioflavin t * fluorescent-probes
OECD category: Biochemistry and molecular biology
Impact factor: 3.9, year: 2022
Method of publishing: Limited access
https://www.sciencedirect.com/science/article/pii/S0300908422003443?via%3Dihub
Permanent Link: https://hdl.handle.net/11104/0351718 - 2.0576802 - BFÚ 2024 RIV NL eng J - Journal Article
Vacek, J. - Zatloukalová, M. - Bartheldyová, E. - Řeha, D. - Minofar, B. - Bednářová, Klára - Renčiuk, Daniel - Coufal, Jan - Fojta, Miroslav - Žádný, Jaroslav - Gessini, A. - Rossi, B. - Storch, Jan - Kabeláč, M.
Hexahelicene DNA-binding: Minor groove selectivity, semi-intercalation and chiral recognition.
International Journal of Biological Macromolecules. Roč. 250, 1 October 2023 (2023), č. článku 125905. ISSN 0141-8130. E-ISSN 1879-0003
R&D Projects: GA TA ČR TA04010082; GA MŠMT EF15_003/0000477
Institutional support: RVO:68081707 ; RVO:67985858
Keywords : Chirality * Nucleic acids * B-DNA double helix * Semi-intercalation * [6]helicene * Imidazolium
OECD category: Organic chemistry; Organic chemistry (UCHP-M)
Impact factor: 8.2, year: 2022
Method of publishing: Limited access
https://www.sciencedirect.com/science/article/pii/S0141813023028003?via%3Dihub
Permanent Link: https://hdl.handle.net/11104/0346205File Download Size Commentary Version Access 1-s2.0-S0141813023028003-main.pdf 0 8.2 MB Publisher’s postprint require - 3.0574520 - BFÚ 2024 RIV US eng J - Journal Article
Love, O. - Galindo-Murillo, R. - Zgarbová, M. - Šponer, Jiří - Jurečka, P. - Cheatham III, T. E.
Assessing the Current State of Amber Force Field Modifications for DNA ,2023 Edition.
Journal of Chemical Theory and Computation. Roč. 19, č. 13 (2023), s. 4299-4307. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA ČR(CZ) GA21-23718S
Institutional support: RVO:68081707
Keywords : MOLECULAR-DYNAMICS SIMULATIONS * PARTICLE MESH EWALD * NUCLEIC-ACIDS
OECD category: Atomic, molecular and chemical physics (physics of atoms and molecules including collision, interaction with radiation, magnetic resonances, Mössbauer effect)
Impact factor: 5.5, year: 2022
Method of publishing: Open access
https://pubs.acs.org/doi/10.1021/acs.jctc.3c00233
Permanent Link: https://hdl.handle.net/11104/0350087 - 4.0572134 - BFÚ 2024 RIV US eng J - Journal Article
Zhang, Zhengyue - Šponer, Jiří - Bussi, G. - Mlýnský, Vojtech - Sulc, P. - Simmons, Ch. R. - Stephanopoulos, N. - Krepl, Miroslav
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations.
Journal of Chemical Information and Modeling. Roč. 63, č. 9 (2023), s. 2794-2809. ISSN 1549-9596. E-ISSN 1549-960X
R&D Projects: GA ČR(CZ) GA21-23718S
Institutional support: RVO:68081707
Keywords : FORCE-FIELD * BRANCH MIGRATION * NUCLEIC-ACIDS
OECD category: Inorganic and nuclear chemistry
Impact factor: 5.6, year: 2022
Method of publishing: Open access
https://pubs.acs.org/doi/10.1021/acs.jcim.3c00358
Permanent Link: https://hdl.handle.net/11104/0349995 - 5.0571531 - BFÚ 2024 RIV US eng J - Journal Article
Kührová, P. - Mlýnský, Vojtech - Otyepka, M. - Šponer, Jiří - Banáš, P.
Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes.
Journal of Chemical Information and Modeling. Roč. 63, č. 7 (2023), s. 2133-2146. ISSN 1549-9596. E-ISSN 1549-960X
R&D Projects: GA ČR(CZ) GA23-05639S
Institutional support: RVO:68081707
Keywords : AMBER FORCE-FIELD * NUCLEIC-ACIDS * CATION-BINDING
OECD category: Analytical chemistry
Impact factor: 5.6, year: 2022
Method of publishing: Open access
https://pubs.acs.org/doi/10.1021/acs.jcim.2c01438
Permanent Link: https://hdl.handle.net/11104/0346082 - 6.0570656 - ÚOCHB 2024 RIV GB eng J - Journal Article
Schrenková, Věra - Para Kkadan, Mohammed Siddhique - Kessler, Jiří - Kapitán, J. - Bouř, Petr
Molecular dynamics and Raman optical activity spectra reveal nucleotide conformation ratios in solution.
Physical Chemistry Chemical Physics. Roč. 25, č. 11 (2023), s. 8198-8208. ISSN 1463-9076. E-ISSN 1463-9084
R&D Projects: GA ČR(CZ) GA22-04669S; GA MŠMT(CZ) EF16_019/0000729
Research Infrastructure: e-INFRA CZ - 90140
Institutional support: RVO:61388963
Keywords : vibrational circular dichroism * nucleic acids * free energies
OECD category: Physical chemistry
Impact factor: 3.3, year: 2022
Method of publishing: Open access
https://doi.org/10.1039/D2CP05756E
Permanent Link: https://hdl.handle.net/11104/0341979 - 7.0569260 - BFÚ 2023 RIV DE eng J - Journal Article
Paloncyova, M. - Pykal, M. - Kührová, P. - Banáš, P. - Šponer, Jiří - Otyepka, M.
Computer Aided Development of Nucleic Acid Applications in Nanotechnologies.
Small. Roč. 18, č. 49 (2022). ISSN 1613-6810. E-ISSN 1613-6829
R&D Projects: GA ČR(CZ) GA21-23718S
Institutional support: RVO:68081707
Keywords : biosensors * force fields * lipid nanoparticles * MD simulations * nucleic acids * nucleic acid templated assemblies
OECD category: Coating and films
Impact factor: 13.3, year: 2022
Method of publishing: Limited access
https://onlinelibrary.wiley.com/doi/10.1002/smll.202204408
Permanent Link: https://hdl.handle.net/11104/0340647 - 8.0569227 - BFÚ 2023 RIV US eng J - Journal Article
Pokorná, Pavlína - Krepl, Miroslav - Campagne, S. - Šponer, Jiří
Conformational Heterogeneity of RNA Stem-Loop Hairpins Bound to FUS-RNA Recognition Motif with Disordered RGG Tail Revealed by Unbiased Molecular Dynamics Simulations.
Journal of Physical Chemistry B. Roč. 126, č. 45 (2022), s. 9207-9221. ISSN 1520-6106. E-ISSN 1520-5207
R&D Projects: GA ČR(CZ) GA20-16554S; GA MŠMT EF15_003/0000477
Institutional support: RVO:68081707
Keywords : FORCE-FIELD * NUCLEIC-ACIDS * AMBER * BACKBONE * BINDING
OECD category: Clinical neurology
Impact factor: 3.3, year: 2022
Method of publishing: Open access
https://pubs.acs.org/doi/10.1021/acs.jpcb.2c06168
Permanent Link: https://hdl.handle.net/11104/0340609 - 9.0557136 - ÚOCHB 2023 CZ eng A - Abstract
Osifová, Zuzana - Šála, Michal - Dračínský, Martin
Hydrogen-bonding interactions of 8-oxopurine nucleobases.
35th NMR Valtice. Central European NMR Meeting. Brno: Tribun EU, 2022 - (Novotný, J.; Marek, R.). C29. ISBN 9788026317173.
[NMR Valtice. Central European NMR Meeting /35./. 24.04.2022-27.04.2022, Valtice]
R&D Projects: GA ČR(CZ) GA22-15374S
Institutional support: RVO:61388963
Keywords : hydrogen bonds * 8-oxopurine * NMR spectroscopy * nucleic acids
OECD category: Organic chemistry
Permanent Link: http://hdl.handle.net/11104/0331194 - 10.0556384 - MBÚ 2023 RIV NL eng J - Journal Article
Fadaei, Fatemeh - Tortora, M. - Gessini, A. - Masciovecchio, C. - Catalini, S. - Vigna, J. - Mancini, I. - Mele, A. - Vacek, J. - Řeha, David - Minofar, Babak - Rossi, B.
Structural specificity of groove binding mechanism between imidazolium-based ionic liquids and DNA revealed by synchrotron-UV Resonance Raman spectroscopy and molecular dynamics simulations.
Journal of Molecular Liquids. Roč. 347, FEB 1 2022 (2022), č. článku 118350. ISSN 0167-7322. E-ISSN 1873-3166
Research Infrastructure: e-INFRA CZ - 90140
Institutional support: RVO:61388971
Keywords : nucleic-acids * minor-groove * initial configurations * temperature-dependence * melting transitions * stability * systems * thermodynamics * localization * solvents * Synchrotron UV Resonance Raman * Molecular dynamics * Ionic liquids * Nucleic acids * Solvation
OECD category: Microbiology
Impact factor: 6, year: 2022
Method of publishing: Limited access
https://www.sciencedirect.com/science/article/pii/S0167732221030750?via%3Dihub
Permanent Link: http://hdl.handle.net/11104/0331345