Search results
- 1.0583260 - BFÚ 2024 RIV US eng J - Journal Article
Mlýnský, Vojtech - Kührová, Petra - Stadlbauer, Petr - Krepl, Miroslav - Otyepka, M. - Banáš, Pavel - Šponer, Jiří
Simple Adjustment of Intranucleotide Base-Phosphate Interaction in the OL3 AMBER Force Field Improves RNA Simulations.
Journal of Chemical Theory and Computation. Roč. 19, č. 22 (2023), s. 8423-8433. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA ČR(CZ) GA23-05639S
Institutional support: RVO:68081707
Keywords : molecular-dynamics simulations * replica exchange * parameters * tetraloops * uucg * nmr * resolution
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.3c00990
Permanent Link: https://hdl.handle.net/11104/0351262 - 2.0557417 - BFÚ 2023 RIV US eng J - Journal Article
Mlýnský, Vojtech - Janecek, M. - Kührová, Petra - Frohlking, T. - Otyepka, M. - Bussi, G. - Banáš, Pavel - Šponer, Jiří
Toward Convergence in Folding Simulations of RNA Tetraloops : Comparison of Enhanced Sampling Techniques and Effects of Force Field Modifications br.
Journal of Chemical Theory and Computation. Roč. 18, č. 4 (2022), s. 2642-2656. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA MŠMT EF15_003/0000477; GA ČR(CZ) GA20-16554S
Institutional support: RVO:68081707
Keywords : free-energy landscape * molecular-dynamics * replica-exchange * tertiary interactions * parameters * hairpins
OECD category: Organic chemistry
Impact factor: 5.5, year: 2022
Method of publishing: Limited access
https://pubs.acs.org/doi/10.1021/acs.jctc.1c01222
Permanent Link: https://hdl.handle.net/11104/0339585 - 3.0554903 - BFÚ 2022 RIV US eng J - Journal Article
Janeček, Michal - Kührová, P. - Mlýnský, Vojtech - Otyepka, Michal - Šponer, Jiří - Banáš, Pavel
W-RESP: Well-Restrained Electrostatic Potential-Derived Charges. Revisiting the Charge Derivation Model.
Journal of Chemical Theory and Computation. Roč. 17, č. 6 (2021), s. 3495-3509. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA ČR(CZ) GA20-16554S
Institutional support: RVO:68081707
Keywords : correlated molecular calculations * gaussian-basis sets * density-functional theory * partial atomic charges * force-field * ab-initio
OECD category: Physical chemistry
Impact factor: 6.578, year: 2021
Method of publishing: Open access
https://pubs.acs.org/doi/10.1021/acs.jctc.0c00976
Permanent Link: http://hdl.handle.net/11104/0329517 - 4.0551530 - BFÚ 2023 RIV GB eng J - Journal Article
Asha, H. - Stadlbauer, Petr - Martinez-Fernandez, L. - Banáš, Pavel - Šponer, Jiří - Improta, R. - Esposito, L.
Early steps of oxidative damage in DNA quadruplexes are position-dependent: Quantum mechanical and molecular dynamics analysis of human telomeric sequence containing ionized guanine.
International Journal of Biological Macromolecules. Roč. 194, JAN 1 2022 (2022), s. 882-894. ISSN 0141-8130. E-ISSN 1879-0003
R&D Projects: GA ČR(CZ) GA21-23718S; GA MŠMT EF15_003/0000477
Institutional support: RVO:68081707
Keywords : monovalent ion parameters * radical-cation transport * one-electron oxidation * circular-dichroism * crystal-structure * laser photolysis * charge-transport
OECD category: Biochemistry and molecular biology
Impact factor: 8.2, year: 2022
Method of publishing: Open access
https://www.sciencedirect.com/science/article/pii/S0141813021025484?via%3Dihub
Permanent Link: https://hdl.handle.net/11104/0336909 - 5.0540054 - BFÚ 2021 RIV US eng J - Journal Article
Mráziková, Klaudia - Mlýnský, Vojtech - Kührová, P. - Pokorná, Pavlína - Kruse, Holger - Krepl, Miroslav - Otyepka, Michal - Banáš, Pavel - Šponer, Jiří
UUCG RNA Tetraloop as a Formidable Force-Field Challenge for MD Simulations.
Journal of Chemical Theory and Computation. Roč. 16, č. 12 (2020), s. 7601-7617. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA ČR(CZ) GA20-16554S; GA MŠMT EF15_003/0000477
Institutional support: RVO:68081707
Keywords : UUCG RNA Tetraloop * Force-Field * MD Simulations
OECD category: Atomic, molecular and chemical physics (physics of atoms and molecules including collision, interaction with radiation, magnetic resonances, Mössbauer effect)
Impact factor: 6.006, year: 2020
Method of publishing: Limited access
https://pubs.acs.org/doi/10.1021/acs.jctc.0c00801
Permanent Link: http://hdl.handle.net/11104/0317722 - 6.0539743 - BFÚ 2021 RIV US eng J - Journal Article
Mlýnský, Vojtech - Kührová, P. - Kuhr, T. - Otyepka, Michal - Bussi, G. - Banáš, Pavel - Šponer, Jiří
Fine-Tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides.
Journal of Chemical Theory and Computation. Roč. 16, č. 6 (2020), s. 3936-3946. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA ČR(CZ) GA20-16554S
Institutional support: RVO:68081707
Keywords : molecular-dynamics simulations * monovalent ion parameters * replica exchange * stacking * energies * nmr
OECD category: Atomic, molecular and chemical physics (physics of atoms and molecules including collision, interaction with radiation, magnetic resonances, Mössbauer effect)
Impact factor: 6.006, year: 2020
Method of publishing: Limited access
https://pubs.acs.org/doi/10.1021/acs.jctc.0c00228
Permanent Link: http://hdl.handle.net/11104/0317442 - 7.0518355 - 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 - 8.0511789 - BFÚ 2020 RIV GB eng J - Journal Article
Suddala, K.C. - Price, I.R. - Dandpat, S.S. - Janeček, Michal - Kührová, P. - Šponer, Jiří - Banáš, Pavel - Ke, A. - Walter, N.G.
Local-to-global signal transduction at the core of a Mn2+ sensing riboswitch.
Nature Communications. Roč. 10, SEP 20 2019 (2019), č. článku 4304. E-ISSN 2041-1723
R&D Projects: GA MŠMT EF15_003/0000477
Institutional support: RVO:68081707
Keywords : molecular-dynamics * eubacteria sense * rna structure * single
OECD category: Biology (theoretical, mathematical, thermal, cryobiology, biological rhythm), Evolutionary biology
Impact factor: 12.121, year: 2019
Method of publishing: Open access
https://www.nature.com/articles/s41467-019-12230-5.pdf
Permanent Link: http://hdl.handle.net/11104/0302037 - 9.0510264 - BFÚ 2020 RIV US eng J - Journal Article
Kührová, P. - Mlýnský, Vojtech - Zgarbová, M. - Krepl, Miroslav - Bussi, G. - Best, R.B. - Otyepka, M. - Šponer, Jiří - Banáš, Pavel
Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions.
Journal of Chemical Theory and Computation. Roč. 15, č. 5 (2019), s. 3288-3305. ISSN 1549-9618. E-ISSN 1549-9626
Institutional support: RVO:68081707
Keywords : molecular-dynamics simulations * monovalent ion parameters * replica-exchange * nucleic-acids * phosphate interactions
OECD category: Physical chemistry
Impact factor: 5.011, year: 2019
Method of publishing: Limited access
https://pubs.acs.org/doi/10.1021/acs.jctc.8b00955
Permanent Link: http://hdl.handle.net/11104/0300779 - 10.0501549 - 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