Search results
- 1.0455892 - BFÚ 2016 RIV US eng J - Journal Article
Kruse, H. - Mládek, Arnošt - Gkionis, Konstantinos - Hansen, A. - Grimme, S. - Šponer, Jiří
Quantum Chemical Benchmark Study on 46 RNA Backbone Families Using a Dinucleotide Unit.
Journal of Chemical Theory and Computation. Roč. 11, č. 10 (2015), s. 4972-4991. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA ČR(CZ) GBP305/12/G034
Institutional support: RVO:68081707
Keywords : MOLECULAR-DYNAMICS SIMULATIONS * DENSITY-FUNCTIONAL THEORY * SUGAR-PHOSPHATE BACKBONE
Subject RIV: BO - Biophysics
Impact factor: 5.301, year: 2015
Permanent Link: http://hdl.handle.net/11104/0256498 - 2.0435465 - BFÚ 2015 RIV US eng J - Journal Article
Mládek, Arnošt - Banáš, P. - Jurečka, P. - Otyepka, M. - Zgarbová, M. - Šponer, Jiří
Energies and 2 '-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations.
Journal of Chemical Theory and Computation. Roč. 10, č. 1 (2014), s. 463-480. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA ČR(CZ) GAP208/12/1878; GA MŠMT(CZ) ED1.1.00/02.0068
Institutional support: RVO:68081707
Keywords : DENSITY-FUNCTIONAL THEORY * SUGAR-PHOSPHATE BACKBONE * QUANTUM-CHEMICAL CALCULATIONS
Subject RIV: BO - Biophysics
Impact factor: 5.498, year: 2014
Permanent Link: http://hdl.handle.net/11104/0239335 - 3.0427956 - BFÚ 2015 RIV US eng J - Journal Article
Gkionis, K. - Kruse, H. - Platts, J. A. - Mládek, Arnošt - Koča, J. - Šponer, Jiří
Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations.
Journal of Chemical Theory and Computation. Roč. 10, č. 3 (2014), s. 1326-1340. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA ČR(CZ) GAP208/11/1822; GA MŠMT(CZ) ED1.1.00/02.0068
Institutional support: RVO:68081707
Keywords : MOLECULAR-DYNAMICS SIMULATIONS * GAUSSIAN-BASIS SETS * TETRAMOLECULAR G-QUADRUPLEXES
Subject RIV: BO - Biophysics
Impact factor: 5.498, year: 2014
Permanent Link: http://hdl.handle.net/11104/0233394 - 4.0422442 - BFÚ 2014 RIV US eng J - Journal Article
Šponer, Jiří - Šponer, Judit E. - Mládek, Arnošt - Jurečka, P. - Banáš, P. - Otyepka, M.
Nature and Magnitude of Aromatic Base Stacking in DNA and RNA: Quantum Chemistry, Molecular Mechanics, and Experiment.
Biopolymers. Roč. 99, č. 12 (2013), s. 978-988. ISSN 0006-3525. E-ISSN 1097-0282
R&D Projects: GA ČR(CZ) GAP208/12/1878; GA ČR(CZ) GAP208/11/1822; GA ČR(CZ) GBP305/12/G034; GA MŠMT(CZ) ED1.1.00/02.0068
Grant - others:GA ČR(CZ) GPP301/11/P558
Program: GP
Institutional support: RVO:68081707
Keywords : NUCLEIC-ACID BASES * DENSITY-FUNCTIONAL THEORY * POTENTIAL-ENERGY SURFACE
Subject RIV: BO - Biophysics
Impact factor: 2.288, year: 2013
Permanent Link: http://hdl.handle.net/11104/0228559 - 5.0422438 - BFÚ 2014 RIV US eng J - Journal Article
Šponer, Jiří (ed.) - Mládek, Arnošt - Špačková, Naďa - Cang, X. - Cheatham III, Thomas E. - Grimme, S.
Relative Stability of Different DNA Guanine Quadruplex Stem Topologies Derived Using Large-Scale Quantum-Chemical Computations.
Journal of the American Chemical Society. Roč. 135, č. 26 (2013), s. 9785-9796. ISSN 0002-7863. E-ISSN 1520-5126
R&D Projects: GA MŠMT(CZ) ED1.1.00/02.0068; GA ČR(CZ) GAP208/11/1822
Institutional research plan: CEZ:AV0Z50040702
Institutional support: RVO:68081707
Keywords : DENSITY-FUNCTIONAL THEORY * MOLECULAR-DYNAMICS SIMULATIONS * SUGAR-PHOSPHATE BACKBONE
Subject RIV: BO - Biophysics
Impact factor: 11.444, year: 2013
Permanent Link: http://hdl.handle.net/11104/0228558 - 6.0399419 - BFÚ 2014 RIV US eng J - Journal Article
Šponer, Jiří - Šponer, Judit E. - Mládek, Arnošt - Banáš, Pavel - Jurečka, P. - Otyepka, Michal
How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists.
Methods. Roč. 64, č. 1 (2013), s. 3-11. ISSN 1046-2023. E-ISSN 1095-9130
R&D Projects: GA MŠMT(CZ) ED1.1.00/02.0068; GA ČR(CZ) GAP208/12/1878; GA ČR(CZ) GBP208/12/G016
Grant - others:GA MŠk(CZ) ED2.1.00/03.0058; GA ČR(CZ) GBP305/12/G034; GA ČR(CZ) GPP301/11/P558
Program: ED; GB; GP
Institutional research plan: CEZ:AV0Z50040702
Institutional support: RVO:68081707
Keywords : DNA structure * Quantum chemistry * Molecular mechanics
Subject RIV: BO - Biophysics
Impact factor: 3.221, year: 2013
Permanent Link: http://hdl.handle.net/11104/0226766 - 7.0392700 - BFÚ 2014 RIV GB eng J - Journal Article
Mládek, Arnošt - Krepl, Miroslav - Svozil, Daniel - Čech, P. - Otyepka, M. - Banáš, P. - Zgarbová, M. - Jurečka, P. - Šponer, Jiří
Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar-phosphate backbone and their comparison with modern density functional theory.
Physical Chemistry Chemical Physics. Roč. 15, č. 19 (2013), s. 7295-7310. ISSN 1463-9076. E-ISSN 1463-9084
R&D Projects: GA ČR(CZ) GAP208/11/1822
Grant - others:GA MŠk(CZ) ED1.1.00/02.0068
Program: ED
Institutional research plan: CEZ:AV0Z50040702
Institutional support: RVO:68081707
Keywords : GAUSSIAN-BASIS SETS * GENERALIZED GRADIENT APPROXIMATION * CORRELATED MOLECULAR CALCULATIONS
Subject RIV: BO - Biophysics
Impact factor: 4.198, year: 2013
Permanent Link: http://hdl.handle.net/11104/0221508 - 8.0392589 - BFÚ 2014 RIV GB eng J - Journal Article
Šponer, Judit E. - Mládek, Arnošt - Šponer, Jiří
Structural and energetic factors controlling the enantioselectivity of dinucleotide formation under prebiotic conditions.
Physical Chemistry Chemical Physics. Roč. 15, č. 17 (2013), s. 6235-6242. ISSN 1463-9076. E-ISSN 1463-9084
R&D Projects: GA ČR GAP208/10/2302
Grant - others:GA MŠk(CZ) ED1.1.00/02.0068
Program: ED
Institutional research plan: CEZ:AV0Z50040702
Institutional support: RVO:68081707
Keywords : APPROXIMATE COULOMB POTENTIALS * PEPTIDE-BOND FORMATION * ZETA VALENCE QUALITY
Subject RIV: BO - Biophysics
Impact factor: 4.198, year: 2013
Permanent Link: http://hdl.handle.net/11104/0221409 - 9.0389600 - BFÚ 2014 RIV US eng J - Journal Article
Ferus, Martin - Civiš, Svatopluk - Mládek, Arnošt - Šponer, Jiří - Juha, Libor - Šponer, Judit E.
On the Road from Formamide Ices to Nucleobases: IR-Spectroscopic Observation of a Direct Reaction between Cyano Radicals and Formamide in a High-Energy Impact Event.
Journal of the American Chemical Society. Roč. 134, č. 51 (2012), s. 20788-20796. ISSN 0002-7863. E-ISSN 1520-5126
R&D Projects: GA ČR(CZ) GAP208/10/2302; GA AV ČR(CZ) IAAX00100903
Institutional research plan: CEZ:AV0Z50040702
Institutional support: RVO:68081707 ; RVO:61388955 ; RVO:68378271
Keywords : HIGH-POWER LASER * APPROXIMATE COULOMB POTENTIALS * INDUCED DIELECTRIC-BREAKDOWN
Subject RIV: BO - Biophysics
Impact factor: 10.677, year: 2012
Permanent Link: http://hdl.handle.net/11104/0218455 - 10.0384735 - BFÚ 2013 RIV GB eng J - Journal Article
Šponer, Jiří - Mládek, Arnošt - Šponer, Judit E. - Svozil, Daniel - Zgarbová, M. - Banáš, Pavel - Jurečka, P. - Otyepka, M.
The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies.
Physical Chemistry Chemical Physics. Roč. 14, č. 44 (2012), s. 15257-15277. ISSN 1463-9076. E-ISSN 1463-9084
R&D Projects: GA ČR(CZ) GD203/09/H046; GA ČR(CZ) GAP208/10/2302; GA ČR(CZ) GAP208/11/1822; GA ČR(CZ) GAP208/12/1878; GA ČR(CZ) GA203/09/1476; GA ČR(CZ) GBP305/12/G034
Institutional research plan: CEZ:AV0Z50040702
Keywords : DNA * RNA * sugar-phosphate backbone
Subject RIV: BO - Biophysics
Impact factor: 3.829, year: 2012
Permanent Link: http://hdl.handle.net/11104/0214279