Search results
- 1.0392513 - ÚOCHB 2014 RIV US eng J - Journal Article
Přecechtělová, J. - Munzarová, M. L. - Vaara, J. - Novotný, J. - Dračínský, Martin - Sklenář, V.
Toward Reproducing Sequence Trends in Phosphorus Chemical Shifts for Nucleic Acids by MD/DFT Calculations.
Journal of Chemical Theory and Computation. Roč. 9, č. 3 (2013), s. 1641-1656. ISSN 1549-9618. E-ISSN 1549-9626
Grant - others:GA MŠk(CZ) LM2010005; GA MŠk(CZ) LC06030
Program: LC
Institutional support: RVO:61388963
Keywords : density-funtional calculations * molecular-dynamics simulations * phosphate group * B-DNA
Subject RIV: CF - Physical ; Theoretical Chemistry
Impact factor: 5.310, year: 2013
Permanent Link: http://hdl.handle.net/11104/0221362 - 2.0379302 - BFÚ 2013 RIV US eng J - Journal Article
Šponer, Judit E. - Mládek, Arnošt - Šponer, Jiří - Fuentes-Cabrera, M.
Formamide-based prebiotic synthesis of nucleobases: A kinetically accessible reaction route.
Journal of Physical Chemistry A. Roč. 116, č. 1 (2012), s. 720-726. ISSN 1089-5639. E-ISSN 1520-5215
R&D Projects: GA MŠMT(CZ) LC06030; GA AV ČR(CZ) IAA400040802; GA ČR(CZ) GAP208/10/2302; GA ČR(CZ) GA203/09/1476; GA ČR(CZ) GAP208/11/1822; GA ČR(CZ) GD203/09/H046
Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702
Keywords : formamide * prebiotic synthesis * nucleobase
Subject RIV: BO - Biophysics
Impact factor: 2.771, year: 2012
Permanent Link: http://hdl.handle.net/11104/0007112 - 3.0378737 - BFÚ 2013 RIV US eng J - Journal Article
Šponer, Judit E. - Šponer, Jiří
Is formamide nature’s choice to create life? Comment on the paper “Formamide and the origin of life“ by Raffaele Saladino et al.
Physics of Life Reviews. Roč. 9, č. 1 (2012), s. 109-110. ISSN 1571-0645. E-ISSN 1873-1457
R&D Projects: GA MŠMT(CZ) LC06030; GA AV ČR(CZ) IAA400040802; GA ČR(CZ) GAP208/10/2302; GA ČR(CZ) GA203/09/1476; GA ČR(CZ) GAP208/11/1822
Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702
Keywords : formamide * prebiotic synthesis * nucleobase
Subject RIV: BO - Biophysics
Impact factor: 6.583, year: 2012
Permanent Link: http://hdl.handle.net/11104/0210137 - 4.0373427 - BFÚ 2012 RIV DE eng J - Journal Article
Kašpárková, Jana - Vojtíšková, Marie - Natile, G. - Brabec, Viktor
Unique properties of DNA interstrand cross-links of antitumor oxaliplatin and the effect of chirality of the carrier ligand.
Chemistry - A European Journal. Roč. 14, č. 4 (2008), s. 1330-1341. ISSN 0947-6539. E-ISSN 1521-3765
R&D Projects: GA ČR(CZ) GA305/05/2030; GA MZd(CZ) NR8562; GA AV ČR(CZ) 1QS500040581
Grant - others:GA MŠk(CZ) LC06030; GA AV ČR(CZ) KAN200200651
Program: LC; KA
Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702
Keywords : antitumor agents * DNA * platinum
Subject RIV: BO - Biophysics
Impact factor: 5.454, year: 2008
Permanent Link: http://hdl.handle.net/11104/0206528 - 5.0373426 - BFÚ 2012 RIV US eng J - Journal Article
Banáš, P. - Hollas, D. - Zgarbová, M. - Jurečka, P. - Orozco, M. - Cheatham III, T.E. - Šponer, Jiří - Otyepka, M.
Performance of molecular mechanics force fields for RNA simulations: Stability of UUCG and GNRA hairpins.
Journal of Chemical Theory and Computation. Roč. 6, č. 12 (2010), s. 3836-3849. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA MŠMT(CZ) LC06030; GA ČR(CZ) GD203/09/H046
Keywords : molecular dynamics * force fields * RNA * tetraloops
Subject RIV: BO - Biophysics
Impact factor: 5.138, year: 2010
Permanent Link: http://hdl.handle.net/11104/0206527 - 6.0373425 - BFÚ 2012 RIV US eng J - Journal Article
Šponer, Jiří - Šponer, Judit E. - Petrov, A.I. - Leontis, N.B.
Quantum chemical studies of nucleic acids: Can we construct a bridge to the RNA structural biology and bioinformatics communities?
Journal of Physical Chemistry B. Roč. 114, č. 48 (2010), s. 15723-15741. ISSN 1520-6106. E-ISSN 1520-5207
R&D Projects: GA MŠMT(CZ) LC06030
Keywords : quantum chemistry * RNA bioinformatics * nucleic acids
Subject RIV: BO - Biophysics
Impact factor: 3.603, year: 2010
Permanent Link: http://hdl.handle.net/11104/0006884 - 7.0373424 - BFÚ 2012 RIV GB eng J - Journal Article
Morgado, Claudio A. - Jurečka, P. - Svozil, D. - Hobza, P. - Šponer, Jiří
Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptions.
Physical Chemistry Chemical Physics. Roč. 12, č. 14 (2010), s. 3522-3534. ISSN 1463-9076. E-ISSN 1463-9084
R&D Projects: GA MŠMT(CZ) LC06030
Keywords : quantum chemistry * stacking * force field
Subject RIV: BO - Biophysics
Impact factor: 3.454, year: 2010
Permanent Link: http://hdl.handle.net/11104/0206526 - 8.0373422 - BFÚ 2012 RIV US eng J - Journal Article
Reshetnikov, R. - Golovin, A. - Spiridonova, V. - Kopylov, A. - Šponer, Jiří
Structural dynamics of thrombin-binding DNA aptamer d(GGTTGGTGTGGTTGG) quadruplex DNA studied by large-scale explicit solvent simulations.
Journal of Chemical Theory and Computation. Roč. 6, č. 10 (2010), s. 3003-3014. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA MŠMT(CZ) LC06030
Keywords : molecular dynamics * quadruplex DNA * thrombin
Subject RIV: BO - Biophysics
Impact factor: 5.138, year: 2010
Permanent Link: http://hdl.handle.net/11104/0206524 - 9.0373421 - BFÚ 2012 RIV US eng J - Journal Article
Banáš, P. - Walter, N.G. - Šponer, Jiří - Otyepka, M.
Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics.
Journal of Physical Chemistry B. Roč. 114, č. 26 (2010), s. 8701-8712. ISSN 1520-6106. E-ISSN 1520-5207
R&D Projects: GA MŠMT(CZ) LC06030; GA ČR(CZ) GA203/09/1476; GA MŠMT(CZ) GD203/09/H046
Keywords : riboswitch * ribozyme * RNA structure * molecular dynamics simulations
Subject RIV: BO - Biophysics
Impact factor: 3.603, year: 2010
Permanent Link: http://hdl.handle.net/11104/0006883 - 10.0373420 - BFÚ 2012 RIV GB eng J - Journal Article
Beššeová, Ivana - Réblová, Kamila - Leontis, N.B. - Šponer, Jiří
Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome.
Nucleic Acids Research. Roč. 38, č. 18 (2010), s. 6247-6264. ISSN 0305-1048. E-ISSN 1362-4962
R&D Projects: GA ČR(CZ) GD203/09/H046; GA MŠMT(CZ) LC06030
Keywords : RNA * molecular dynamics * three-way junction
Subject RIV: BO - Biophysics
Impact factor: 7.836, year: 2010
Permanent Link: http://hdl.handle.net/11104/0206523