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 - 2.0574517 - BFÚ 2024 RIV US eng J - Journal Article
Voegele, J. - Duchardt-Ferner, E. - Kruse, Holger - Zhang, Zhengyue - Šponer, Jiří - Krepl, Miroslav - Woehnert, J.
Structural and dynamic effects of pseudouridine modifications on noncanonical interactions in RNA.
RNA. Roč. 29, č. 6 (2023), s. 790-807. ISSN 1355-8382. E-ISSN 1469-9001
R&D Projects: GA ČR(CZ) GA23-05639S
Institutional support: RVO:68081707
Keywords : pseudouridine * RNA structure * U-turn * U base pair * nmr * MD simulations
OECD category: Biochemistry and molecular biology
Impact factor: 4.5, year: 2022
Method of publishing: Limited access
https://rnajournal.cshlp.org/content/29/6/790
Permanent Link: https://hdl.handle.net/11104/0350076 - 3.0571531 - 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