Search results
- 1.0598262 - BFÚ 2025 RIV CH eng J - Journal Article
Saladino, R. - Šponer, Judit E. - Šponer, Jiří - Costanzo, G. - Pino, S. - Di Mauro, E.
Chemomimesis and Molecular Darwinism in Action: From Abiotic Generation of Nucleobases to Nucleosides and RNA.
Life. Roč. 8, č. 2 (2018), č. článku 24. E-ISSN 2075-1729
R&D Projects: GA ČR GA17-05076S
Institutional support: RVO:68081707
Keywords : high-energy chemistry * prebiotic synthesis * differential stability * organic-molecules * systems chemistry * borate minerals * nucleic-acids * amino-acids
OECD category: Microbiology
Method of publishing: Open access
https://www.mdpi.com/2075-1729/8/2/24
Permanent Link: https://hdl.handle.net/11104/0355986 - 2.0586924 - ÚOCHB 2025 RIV US eng J - Journal Article
Volek, Martin - Kurfürst, Jaroslav - Kožíšek, Milan - Srb, Pavel - Veverka, Václav - Curtis, Edward A.
Apollon: a deoxyribozyme that generates a yellow product.
Nucleic Acids Research. Roč. 52, č. 15 (2024), s. 9062-9075, č. článku gkae490. ISSN 0305-1048. E-ISSN 1362-4962
R&D Projects: GA ČR(CZ) GA24-11210S; GA MŠMT(CZ) EH22_008/0004575
Institutional support: RVO:61388963
Keywords : in-vitro * secondary structure * nucleic-acids
Impact factor: 16.6, year: 2023
Method of publishing: Open access
https://doi.org/10.1093/nar/gkae490
Permanent Link: https://hdl.handle.net/11104/0354293File Download Size Commentary Version Access 10.1093nargkae490.pdf 3 2.2 MB Publisher’s postprint open-access - 3.0584664 - BFÚ 2025 RIV NL eng J - Journal Article
Pokorná, Pavlína - Mlýnský, Vojtech - Bussi, G. - Šponer, Jiří - Stadlbauer, Petr
Molecular dynamics simulations reveal the parallel stranded d (GGGA)3GGG DNA quadruplex folds via multiple paths from a coil-like ensemble.
International Journal of Biological Macromolecules. Roč. 261, 2024-03-22 (2024), č. článku 129712. ISSN 0141-8130. E-ISSN 1879-0003
R&D Projects: GA ČR(CZ) GA21-23718S
Institutional support: RVO:68081707
Keywords : amber force-field * nucleic-acids * g-triplex * energy landscape * human telomere * pathways * rna * stability * sequence * insights * G-Quadruplex
OECD category: Biochemistry and molecular biology
Impact factor: 7.7, year: 2023
Method of publishing: Open access
https://www.sciencedirect.com/science/article/pii/S0141813024005154?via%3Dihub
Permanent Link: https://hdl.handle.net/11104/0355021 - 4.0583721 - 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: 3.3, year: 2023
Method of publishing: Limited access
https://www.sciencedirect.com/science/article/pii/S0300908422003443?via%3Dihub
Permanent Link: https://hdl.handle.net/11104/0351718 - 5.0576802 - 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: 7.7, year: 2023
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 - 6.0574520 - 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: 5.7, year: 2023
Method of publishing: Open access
https://pubs.acs.org/doi/10.1021/acs.jctc.3c00233
Permanent Link: https://hdl.handle.net/11104/0350087 - 7.0572134 - 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: 2023
Method of publishing: Open access
https://pubs.acs.org/doi/10.1021/acs.jcim.3c00358
Permanent Link: https://hdl.handle.net/11104/0349995 - 8.0571531 - 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: 2023
Method of publishing: Open access
https://pubs.acs.org/doi/10.1021/acs.jcim.2c01438
Permanent Link: https://hdl.handle.net/11104/0346082 - 9.0570656 - 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: 2.9, year: 2023
Method of publishing: Open access
https://doi.org/10.1039/D2CP05756E
Permanent Link: https://hdl.handle.net/11104/0341979 - 10.0569260 - 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