Search results
- 1.0574520 - 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 - 2.0562866 - ÚOCHB 2023 RIV US eng J - Journal Article
Fukal, Jiří - Zgarbová, M. - Jurečka, P. - Šebera, Jakub - Sychrovský, Vladimír
Probabilistic Interpretation of NMR J-Couplings Determines BI-BII State Equilibria in DNA.
Journal of Chemical Theory and Computation. Roč. 18, č. 11 (2022), s. 6989-6999. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA ČR(CZ) GA19-13436S
Research Infrastructure: e-INFRA CZ - 90140
Institutional support: RVO:61388963
Keywords : molecular dynamics simulations * phosphorus chemical shifts * nucleic acid backbone
OECD category: Biophysics
Impact factor: 5.5, year: 2022
Method of publishing: Limited access
https://doi.org/10.1021/acs.jctc.2c00733
Permanent Link: https://hdl.handle.net/11104/0335048 - 3.0554454 - BFÚ 2022 RIV US eng J - Journal Article
Zgarbová, M. - Šponer, Jiří - Jurečka, P.
Z-DNA as a Touchstone for Additive Empirical Force Fields and a Refinement of the Alpha/Gamma DNA Torsions for AMBER.
Journal of Chemical Theory and Computation. Roč. 17, č. 10 (2021), s. 6292-6301. ISSN 1549-9618. E-ISSN 1549-9626
Institutional support: RVO:68081707
Keywords : molecular-dynamics simulations * basis-set convergence * nucleic-acids * dihedral parameters * rna
OECD category: Physical chemistry
Impact factor: 6.578, year: 2021
Method of publishing: Open access with time embargo
https://pubs.acs.org/doi/10.1021/acs.jctc.1c00697
Permanent Link: http://hdl.handle.net/11104/0329163 - 4.0547591 - ÚOCHB 2023 RIV US eng J - Journal Article
Fukal, Jiří - Buděšínský, Miloš - Páv, Ondřej - Jurečka, P. - Zgarbová, M. - Šebera, Jakub - Sychrovský, Vladimír
The Ad-MD method to calculate NMR shift including effects due to conformational dynamics: The 31P NMR shift in DNA.
Journal of Computational Chemistry. Roč. 43, č. 2 (2022), s. 132-143. ISSN 0192-8651. E-ISSN 1096-987X
R&D Projects: GA ČR(CZ) GA19-13436S
Research Infrastructure: e-INFRA CZ - 90140
Institutional support: RVO:61388963
Keywords : 31P NMR shift * DNA phosphate * MD averaging
OECD category: Biophysics
Impact factor: 3, year: 2022
Method of publishing: Limited access
https://doi.org/10.1002/jcc.26778
Permanent Link: http://hdl.handle.net/11104/0323804 - 5.0510264 - 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 - 6.0477377 - BFÚ 2018 RIV US eng J - Journal Article
Zgarbová, M. - Jurečka, P. - Lankaš, F. - Cheatham, T. E. - Šponer, Jiří - Otyepka, M.
Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences.
Journal of Chemical Information and Modeling. Roč. 57, č. 2 (2017), s. 275-287. ISSN 1549-9596. E-ISSN 1549-960X
Grant - others:GA ČR(CZ) GP14-29874P; GA MŠk(CZ) LO1305
Institutional support: RVO:68081707
Keywords : molecular-dynamics simulations * amber force-field * t-g-g * b-dna
OECD category: Physical chemistry
Impact factor: 3.804, year: 2017
Permanent Link: http://hdl.handle.net/11104/0273870 - 7.0476549 - BFÚ 2018 RIV US eng J - Journal Article
Zgarbová, M. - Jurečka, P. - Banáš, P. - Havrila, Marek - Šponer, Jiří - Otyepka, M.
Noncanonical alpha/gamma Backbone Conformations in RNA and the Accuracy of Their Description by the AMBER Force Field.
Journal of Physical Chemistry B. Roč. 121, č. 11 (2017), s. 2420-2433. ISSN 1520-6106. E-ISSN 1520-5207
Institutional support: RVO:68081707
Keywords : molecular-dynamics simulations * sugar-phosphate backbone * free-energy landscape * ribosomal-rna
OECD category: Physical chemistry
Impact factor: 3.146, year: 2017
Permanent Link: http://hdl.handle.net/11104/0273031 - 8.0476273 - BFÚ 2018 RIV GB eng J - Journal Article
Šponer, Jiří - Krepl, Miroslav - Banáš, P. - Kührová, P. - Zgarbová, M. - Jurečka, P. - Havrila, Marek - Otyepka, M.
How to understand atomistic molecular dynamics simulations of RNA and protein-RNA complexes?
Wiley Interdisciplinary Reviews-RNA. Roč. 8, č. 3 (2017), č. článku e1405. ISSN 1757-7004. E-ISSN 1757-7012
R&D Projects: GA ČR(CZ) GBP305/12/G034
Grant - others:GA MŠk(CZ) LO1305
Institutional support: RVO:68081707
Keywords : hepatitis-delta-virus * amber force-field * free-energy landscape * hdv ribozyme
OECD category: Physical chemistry
Impact factor: 5.844, year: 2017
Permanent Link: http://hdl.handle.net/11104/0272813 - 9.0471964 - BFÚ 2017 RIV US eng J - Journal Article
Galindo-Murillo, R. - Robertson, J. - Zgarbová, M. - Šponer, Jiří - Otyepka, M. - Jurečka, P. - Cheatham III, T. E.
Assessing the Current State of Amber Force Field Modifications for DNA.
Journal of Chemical Theory and Computation. Roč. 12, č. 8 (2016), s. 4114-4127. ISSN 1549-9618. E-ISSN 1549-9626
Institutional support: RVO:68081707
Keywords : molecular-dynamics simulations * particle mesh ewald * pair opening kinetics
Subject RIV: BO - Biophysics
Impact factor: 5.245, year: 2016
Permanent Link: http://hdl.handle.net/11104/0269324 - 10.0458973 - ÚOCHB 2017 RIV US eng J - Journal Article
Dršata, Tomáš - Zgarbová, M. - Jurečka, P. - Šponer, Jiří - Lankaš, Filip
On the Use of Molecular Dynamics Simulations for Probing Allostery through DNA.
Biophysical Journal. Roč. 110, č. 4 (2016), s. 874-876. ISSN 0006-3495. E-ISSN 1542-0086
R&D Projects: GA ČR(CZ) GA14-21893S
Institutional support: RVO:61388963 ; RVO:68081707
Keywords : B-DNA * modulation
Subject RIV: BO - Biophysics
Impact factor: 3.656, year: 2016
Permanent Link: http://hdl.handle.net/11104/0259175