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 - 2.0569826 - BFÚ 2023 RIV GB eng J - Journal Article
Krepl, Miroslav - Pokorná, Pavlína - Mlýnský, Vojtech - Stadlbauer, Petr - Šponer, Jiří
Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field.
Nucleic Acids Research. Roč. 50, č. 21 (2022), s. 12480-12496. ISSN 0305-1048. E-ISSN 1362-4962
R&D Projects: GA ČR(CZ) GA20-16554S; GA MŠMT EF15_003/0000477
Institutional support: RVO:68081707
Keywords : MOLECULAR-DYNAMICS SIMULATIONS * REPLICA EXCHANGE * RECOGNITION MOTIFS
OECD category: Biochemistry and molecular biology
Impact factor: 14.9, year: 2022
Method of publishing: Limited access
https://academic.oup.com/nar/article/50/21/12480/6858795?login=true
Permanent Link: https://hdl.handle.net/11104/0341159 - 3.0557417 - 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 - 4.0540713 - BFÚ 2021 RIV GB eng J - Journal Article
Šponer, Jiří - Islam, B. - Stadlbauer, Petr - Haider, S.
Molecular dynamics simulations of G-quadruplexes: The basic principles and their application to folding and ligand binding.
Annual Reports in Medicinal Chemistry. Roč. 54, č. 2020 (2020), s. 197-241. ISSN 0065-7743
R&D Projects: GA MŠMT EF15_003/0000477
Institutional support: RVO:68081707
Keywords : telomeric g-quadruplex * free-energy calculations * amber force-field * quantum-chemical computations * replica-exchange
OECD category: Biochemistry and molecular biology
Impact factor: 1.059, year: 2020
Method of publishing: Limited access
https://www.sciencedirect.com/science/article/pii/S0065774320300154?via%3Dihub
Permanent Link: http://hdl.handle.net/11104/0318331 - 5.0539743 - 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 - 6.0521326 - BTÚ 2020 RIV CH eng J - Journal Article
Peter, Emanuel K. - Černý, Jiří
A Hybrid Hamiltonian for the Accelerated Sampling along Experimental Restraints.
International Journal of Molecular Sciences. Roč. 20, č. 2 (2019), č. článku 370. E-ISSN 1422-0067
R&D Projects: GA MŠMT(CZ) LM2015047; GA MŠMT(CZ) ED1.1.00/02.0109; GA MŠMT(CZ) EF16_013/0001777
Institutional support: RVO:86652036
Keywords : molecular-dynamics simulation * free-energy landscapes * monte-carlo simulations * replica-exchange method
OECD category: Biochemistry and molecular biology
Impact factor: 4.556, year: 2019
Method of publishing: Open access
https://www.mdpi.com/1422-0067/20/2/370
Permanent Link: http://hdl.handle.net/11104/0305957 - 7.0510264 - 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 - 8.0501653 - BFÚ 2019 RIV US eng J - Journal Article
Bochicchio, A. - Krepl, Miroslav - Yang, F. - Varani, G. - Šponer, Jiří - Carloni, P.
Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study.
PLoS Computational Biology. Roč. 14, č. 12 (2018), č. článku e1006642. ISSN 1553-734X. E-ISSN 1553-7358
R&D Projects: GA ČR(CZ) GBP305/12/G034
Institutional support: RVO:68081707
Keywords : hamiltonian replica exchange * protein-structure * swiss-model * binding
OECD category: Biochemistry and molecular biology
Impact factor: 4.428, year: 2018
Permanent Link: http://hdl.handle.net/11104/0293645 - 9.0435961 - BFÚ 2015 RIV US eng J - Journal Article
Šponer, Jiří - Banáš, P. - Jurečka, P. - Zgarbová, M. - Kührová, P. - Havrila, Marek - Krepl, Miroslav - Stadlbauer, Petr - Otyepka, M.
Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome.
Journal of Physical Chemistry Letters. Roč. 5, č. 10 (2014), s. 1771-1782. ISSN 1948-7185
R&D Projects: GA ČR(CZ) GAP208/12/1878
Institutional support: RVO:68081707
Keywords : DELTA-VIRUS RIBOZYME * AMBER FORCE-FIELD * REPLICA-EXCHANGE METHOD
Subject RIV: BO - Biophysics
Impact factor: 7.458, year: 2014
Permanent Link: http://hdl.handle.net/11104/0239809