Search results
- 1.0518355 - BFÚ 2020 RIV GB eng J - Journal Article
Stadlbauer, Petr - Kührová, P. - Vicherek, L. - Banáš, Pavel - Otyepka, Michal - Trantírek, Lukáš - Šponer, Jiří
Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes.
Nucleic Acids Research. Roč. 47, č. 14 (2019), s. 7276-7293. ISSN 0305-1048. E-ISSN 1362-4962
R&D Projects: GA ČR(CZ) GA16-13721S; GA ČR GA17-12075S; GA MŠMT EF15_003/0000477
Institutional support: RVO:68081707
Keywords : telomeric g-quadruplex * amber force-field * monovalent ion parameters * single-molecule fret * particle mesh ewald * nucleic-acids
OECD category: Biochemistry and molecular biology
Impact factor: 11.502, year: 2019
Method of publishing: Open access
https://academic.oup.com/nar/article-pdf/47/14/7276/29185953/gkz610.pdf
Permanent Link: http://hdl.handle.net/11104/0303512 - 2.0502419 - BFÚ 2019 RIV GB eng J - Journal Article
Havrila, Marek - Stadlbauer, Petr - Kührová, P. - Banáš, P. - Mergny, Jean-Louis - Otyepka, Michal - Šponer, Jiří
Structural dynamics of propeller loop: towards folding of RNA G-quadruplex.
Nucleic Acids Research. Roč. 46, č. 17 (2018), s. 8754-8771. ISSN 0305-1048. E-ISSN 1362-4962
R&D Projects: GA MŠMT EF15_003/0000477; GA ČR(CZ) GA16-13721S
Institutional support: RVO:68081707
Keywords : telomeric g-quadruplex * monovalent ion parameters * particle mesh ewald * molecular-dynamics
OECD category: Biochemistry and molecular biology
Impact factor: 11.147, year: 2018
Permanent Link: http://hdl.handle.net/11104/0294352 - 3.0502248 - BFÚ 2019 RIV US eng J - Journal Article
Islam, Barira - Stadlbauer, Petr - Krepl, Miroslav - Havrila, Marek - Haider, S. - Šponer, Jiří
Structural Dynamics of Lateral and Diagonal Loops of Human Telomeric G-Quadruplexes in Extended MD Simulations.
Journal of Chemical Theory and Computation. Roč. 14, č. 10 (2018), s. 5011-5026. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA ČR(CZ) GA16-13721S; GA MŠMT EF15_003/0000477
Institutional support: RVO:68081707
Keywords : amber force-field * monovalent ion parameters * molecular-dynamics * nucleic-acids
OECD category: Physical chemistry
Impact factor: 5.313, year: 2018
Permanent Link: http://hdl.handle.net/11104/0294198 - 4.0501656 - BFÚ 2019 RIV US eng J - Journal Article
Chen, J. - Zhang, Y. - Cheng, M. - Guo, Y. - Šponer, Jiří - Monchaud, D. - Mergny, Jean-Louis - Ju, H. - Zhou, J.
How Proximal Nucleobases Regulate the Catalytic Activity of G-Quadruplex/Hemin DNAzymes.
ACS Catalysis. Roč. 8, č. 12 (2018), s. 11352-11361. ISSN 2155-5435. E-ISSN 2155-5435
R&D Projects: GA ČR(CZ) GA16-13721S; GA MŠMT EF15_003/0000477
Institutional support: RVO:68081707
Keywords : repair thymine dimers * peroxidase-activity * activity enhancement * binding-site
OECD category: Physical chemistry
Impact factor: 12.221, year: 2018
Permanent Link: http://hdl.handle.net/11104/0293649 - 5.0501549 - BFÚ 2019 RIV US eng J - Journal Article
Kruse, Holger - Banáš, Pavel - Šponer, Jiří
Investigations of Stacked DNA Base-Pair Steps: Highly Accurate Stacking Interaction Energies, Energy Decomposition, and Many-Body Stacking Effects.
Journal of Chemical Theory and Computation. Roč. 15, č. 1 (2019), s. 95-115. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA MŠMT EF15_003/0000477; GA ČR(CZ) GA16-13721S
Institutional support: RVO:68081707
Keywords : density-functional theory * generalized gradient approximation * main-group thermochemistry * nonempirical ab-initio
OECD category: Physical chemistry
Impact factor: 5.011, year: 2019
Method of publishing: Limited access
https://pubs.acs.org/doi/10.1021/acs.jctc.8b00643
Permanent Link: http://hdl.handle.net/11104/0293561 - 6.0495173 - BFÚ 2019 RIV US eng J - Journal Article
Kruse, Holger - Šponer, Jiří
Highly accurate equilibrium structure of the C2h symmetric N1-to-O2 hydrogen-bonded uracil-dimer.
International Journal of Quantum Chemistry. Roč. 118, č. 15 (2018), č. článku e25624. ISSN 0020-7608. E-ISSN 1097-461X
R&D Projects: GA MŠMT EF15_003/0000477; GA ČR(CZ) GA16-13721S
Institutional support: RVO:68081707
Keywords : density-functional theory * dispersion correction * noncovalent interactions * base-pairs * basis-sets * gas-phase * geometries * molecules * thermochemistry * formamide
OECD category: Physical chemistry
Impact factor: 2.263, year: 2018
Permanent Link: http://hdl.handle.net/11104/0288181 - 7.0492425 - BFÚ 2019 RIV GB eng J - Journal Article
Szabla, Rafal - Kruse, Holger - Stadlbauer, Petr - Šponer, Jiří - Sobolewski, A. L.
Sequential electron transfer governs the UV-induced self-repair of DNA photolesions.
Chemical Science. Roč. 9, č. 12 (2018), s. 3131-3140. ISSN 2041-6520. E-ISSN 2041-6539
R&D Projects: GA ČR(CZ) GA16-13721S
Institutional support: RVO:68081707
Keywords : amber force-field * molecular-dynamics simulations * excited-state dynamics * charge-transfer states
OECD category: Biochemistry and molecular biology
Impact factor: 9.556, year: 2018
Permanent Link: http://hdl.handle.net/11104/0285974 - 8.0486065 - BFÚ 2018 RIV US eng J - Journal Article
Cragnolini, T. - Chakraborty, D. - Šponer, Jiří - Derreumaux, P. - Pasquali, S. - Wales, D.J.
Multifunctional energy landscape for a DNA G-quadruplex: An evolved molecular switch.
Journal of Chemical Physics. Roč. 147, č. 15 (2017), č. článku 152715. ISSN 0021-9606. E-ISSN 1089-7690
R&D Projects: GA ČR(CZ) GA16-13721S
Institutional support: RVO:68081707
Keywords : telomeric g-quadruplex * gb1 hairpin peptide
OECD category: Physical chemistry
Impact factor: 2.843, year: 2017
Permanent Link: http://hdl.handle.net/11104/0280952 - 9.0485739 - BFÚ 2018 RIV NL eng J - Journal Article
Šponer, Jiří - Bussi, G. - Stadlbauer, Petr - Kührová, P. - Banáš, P. - Islam, Barira - Haider, S. - Neidle, S. - Otyepka, M.
Folding of guanine quadruplex molecules-funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies.
Biochimica et Biophysica Acta-General Subjects. Roč. 1861, č. 5 (2017), s. 1246-1263. ISSN 0304-4165. E-ISSN 1872-8006
R&D Projects: GA ČR(CZ) GA16-13721S
Institutional support: RVO:68081707
Keywords : telomeric g-quadruplex * parallel g-quadruplex
OECD category: Biochemistry and molecular biology
Impact factor: 3.679, year: 2017
Permanent Link: http://hdl.handle.net/11104/0280684 - 10.0485734 - BFÚ 2018 RIV US eng J - Journal Article
Islam, Barira - Stadlbauer, Petr - Gil-Ley, A. - Perez-Hernandez, J. A. - Haider, S.M. - Neidle, S. - Bussi, G. - Banáš, P. - Otyepka, Michal - Šponer, Jiří
Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations.
Journal of Chemical Theory and Computation. Roč. 13, č. 6 (2017), s. 2458-2480. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA ČR(CZ) GA16-13721S
Institutional support: RVO:68081707
Keywords : amber force-field * particle mesh ewald
OECD category: Physical chemistry
Impact factor: 5.399, year: 2017
Permanent Link: http://hdl.handle.net/11104/0280681