Search results
- 1.0486054 - BFÚ 2018 RIV US eng J - Journal Article
Mlýnský, V. - Kührová, P. - Jurečka, P. - Šponer, Jiří - Otyepka, M. - Banáš, Pavel
Mapping the Chemical Space of the RNA Cleavage and Its Implications for Ribozyme Catalysis.
Journal of Physical Chemistry B. Roč. 121, č. 48 (2017), s. 10828-10840. ISSN 1520-6106. E-ISSN 1520-5207
R&D Projects: GA ČR GAP208/12/1878
Institutional support: RVO:68081707
Keywords : delta-virus ribozyme * self-cleaving ribozymes
OECD category: Physical chemistry
Impact factor: 3.146, year: 2017
Permanent Link: http://hdl.handle.net/11104/0280942 - 2.0476541 - BFÚ 2018 RIV GB eng J - Journal Article
Figiel, M. - Krepl, Miroslav - Poznanski, J. - Gotab, A. - Šponer, Jiří - Nowotny, M.
Coordination between the polymerase and RNase H activity of HIV-1 reverse transcriptase.
Nucleic Acids Research. Roč. 45, č. 6 (2017), s. 3341-3352. ISSN 0305-1048. E-ISSN 1362-4962
R&D Projects: GA ČR GAP208/12/1878
Grant - others:GA MŠk(CZ) LO1305
Institutional support: RVO:68081707
Keywords : human-immunodeficiency-virus * rna/dna hybrid * force-field
OECD category: Biochemistry and molecular biology
Impact factor: 11.561, year: 2017
Permanent Link: http://hdl.handle.net/11104/0273021 - 3.0471959 - BFÚ 2017 RIV US eng J - Journal Article
Kührová, P. - Best, R.B. - Bottaro, S. - Bussi, G. - Šponer, Jiří - Otyepka, Michal - Banáš, Pavel
Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies.
Journal of Chemical Theory and Computation. Roč. 12, č. 9 (2016), s. 4534-4548. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA ČR GAP208/12/1878
Institutional support: RVO:68081707
Keywords : molecular-dynamics simulations * base-pairs * tertiary interactions * explicit-solvent
Subject RIV: BO - Biophysics
Impact factor: 5.245, year: 2016
Permanent Link: http://hdl.handle.net/11104/0269320 - 4.0471952 - BFÚ 2017 RIV US eng J - Journal Article
Bottaro, S. - Banáš, Pavel - Šponer, Jiří - Bussi, G.
Free Energy Landscape of GAGA and UUCG RNA Tetraloops.
Journal of Physical Chemistry Letters. Roč. 7, č. 20 (2016), s. 4032-4038. ISSN 1948-7185
R&D Projects: GA ČR GAP208/12/1878
Institutional support: RVO:68081707
Keywords : molecular-dynamics simulations * amber force-field * secondary structure * nmr relaxation
Subject RIV: BO - Biophysics
Impact factor: 9.353, year: 2016
Permanent Link: http://hdl.handle.net/11104/0269313 - 5.0457647 - BFÚ 2016 RIV GB eng J - Journal Article
Sripathi, K.N. - Banáš, P. - Réblová, K. - Šponer, Jiří - Otyepka, M. - Walter, Nils G.
Wobble pairs of the HDV ribozyme play specific roles in stabilization of active site dynamics.
Physical Chemistry Chemical Physics. Roč. 17, č. 8 (2015), s. 5887-5900. ISSN 1463-9076. E-ISSN 1463-9084
R&D Projects: GA ČR GAP208/12/1878
Institutional support: RVO:68081707
Keywords : HEPATITIS-DELTA-VIRUS * SELF-CLEAVING RIBOZYMES * ACID-BASE CATALYSIS
Subject RIV: BO - Biophysics
Impact factor: 4.449, year: 2015
Permanent Link: http://hdl.handle.net/11104/0258043 - 6.0447671 - ÚOCHB 2016 RIV US eng J - Journal Article
Haldar, Susanta - Kührová, P. - Banáš, P. - Spiwok, V. - Šponer, Jiří - Hobza, Pavel - Otyepka, M.
Insights into Stability and Folding of GNRA and UNCG Tetra loops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics.
Journal of Chemical Theory and Computation. Roč. 11, č. 8 (2015), s. 3866-3877. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA ČR GAP208/12/1878; GA ČR GBP208/12/G016
Grant - others:GA MŠk(CZ) ED2.1.00/03.0058; GA MŠk(CZ) EE2.3.20.0058; GA MŠk(CZ) EE2.3.20.0155; GA MŠk(CZ) LO1305
Program: ED
Institutional support: RVO:61388963 ; RVO:68081707
Keywords : free energy landscape * di-GMP riboswitch * RNA hairpins
Subject RIV: CF - Physical ; Theoretical Chemistry
Impact factor: 5.301, year: 2015
Permanent Link: http://hdl.handle.net/11104/0249449 - 7.0447582 - BFÚ 2016 RIV US eng J - Journal Article
Dubecký, M. - Walter, Nils G. - Šponer, Jiří - Otyepka, M. - Banáš, Pavel
Chemical Feasibility of the General Acid/Base Mechanism of glmS Ribozyme Self-Cleavage.
Biopolymers. Roč. 103, č. 10 (2015), s. 550-562. ISSN 0006-3525. E-ISSN 1097-0282
R&D Projects: GA MŠMT(CZ) ED1.1.00/02.0068; GA ČR(CZ) GAP208/12/1878
Institutional support: RVO:68081707
Keywords : MOLECULAR-DYNAMICS SIMULATIONS * ACTIVE-SITE GUANINE * HAIRPIN RIBOZYME
Subject RIV: BO - Biophysics
Impact factor: 2.248, year: 2015
Permanent Link: http://hdl.handle.net/11104/0249403 - 8.0446310 - BFÚ 2016 RIV US eng J - Journal Article
Mlýnský, V. - Kuehrova, P. - Zgarbová, M. - Jurečka, P. - Walter, Nils G. - Otyepka, M. - Šponer, Jiří - Banáš, Pavel
Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with epsilon/zeta Force Field Reparametrizations.
Journal of Physical Chemistry B. Roč. 119, č. 11 (2015), s. 4220-4229. ISSN 1520-6106. E-ISSN 1520-5207
R&D Projects: GA ČR(CZ) GAP208/12/1878
Institutional support: RVO:68081707
Keywords : ACID-BASE CATALYSIS * NUCLEIC-ACIDS * RNA CATALYSIS
Subject RIV: BO - Biophysics
Impact factor: 3.187, year: 2015
Permanent Link: http://hdl.handle.net/11104/0248296 - 9.0446303 - BFÚ 2016 RIV NL eng J - Journal Article
Estarellas, C. - Otyepka, M. - Koča, J. - Banáš, P. - Krepl, Miroslav - Šponer, Jiří
Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease.
Biochimica et Biophysica Acta-General Subjects. Roč. 1850, č. 5 (2015), s. 1072-1090. ISSN 0304-4165. E-ISSN 1872-8006
R&D Projects: GA ČR(CZ) GAP208/12/1878; GA MŠMT(CZ) ED1.1.00/02.0068
Institutional support: RVO:68081707
Keywords : CLASSICAL DRUDE OSCILLATOR * SUGAR-PHOSPHATE BACKBONE * POLARIZABLE FORCE-FIELD
Subject RIV: BO - Biophysics
Impact factor: 5.083, year: 2015
Permanent Link: http://hdl.handle.net/11104/0248299 - 10.0442423 - BFÚ 2015 RIV GB eng J - Journal Article
Mlýnský, V. - Walter, Nils G. - Šponer, Jiří - Otyepka, Michal - Banáš, Pavel
The role of an active site Mg2+ in HDV ribozyme self-cleavage: insights from QM/MM calculations.
Physical Chemistry Chemical Physics. Roč. 17, č. 1 (2015), s. 670-679. ISSN 1463-9076. E-ISSN 1463-9084
R&D Projects: GA ČR(CZ) GAP208/12/1878
Institutional support: RVO:68081707
Keywords : HEPATITIS-DELTA-VIRUS * MOLECULAR-DYNAMICS SIMULATIONS * 2'-HYDROXYL GROUP
Subject RIV: BO - Biophysics
Impact factor: 4.449, year: 2015
Permanent Link: http://hdl.handle.net/11104/0245238