Search results
- 1.0471972 - BFÚ 2017 RIV US eng J - Journal Article
Gkionis, Konstantinos - Kruse, Holger - Šponer, Jiří
Derivation of Reliable Geometries in QM Calculations of DNA Structures: Explicit Solvent QM/MM and Restrained Implicit Solvent QM Optimizations of G-Quadruplexes.
Journal of Chemical Theory and Computation. Roč. 12, č. 4 (2016), s. 2000-2016. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA ČR(CZ) GAP208/11/1822
Institutional support: RVO:68081707
Keywords : molecular-dynamics simulations * quantum-chemical computations * continuum solvation models
Subject RIV: BO - Biophysics
Impact factor: 5.245, year: 2016
Permanent Link: http://hdl.handle.net/11104/0269331 - 2.0456571 - BFÚ 2016 US eng J - Journal Article
Zhang, X.J. - Xu, C.X. - Di Felice, R. - Šponer, Jiří - Islam, B. - Stadlbauer, Petr - Ding, Y. - Mao, L. - Mao, Z.W. - Qin, P.Z.
Conformations of Human Telomeric G-Quadruplex Studied Using a Nucleotide-Independent Nitroxide Label.
Biochemistry. Roč. 55, č. 2 (2016), s. 360-372. ISSN 0006-2960
R&D Projects: GA ČR(CZ) GAP208/11/1822; GA MŠMT(CZ) ED1.1.00/02.0068
Institutional support: RVO:68081707
Keywords : PARAMAGNETIC-RESONANCE SPECTROSCOPY * AMBER FORCE-FIELD * NUCLEIC-ACIDS
Subject RIV: BO - Biophysics
Impact factor: 2.938, year: 2016
Permanent Link: http://hdl.handle.net/11104/0257128 - 3.0456040 - BFÚ 2016 RIV GB eng J - Journal Article
Stadlbauer, Petr - Kuehrova, P. - Banáš, P. - Koča, J. - Bussi, G. - Trantírek, L. - Otyepka, M. - Šponer, Jiří
Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations.
Nucleic Acids Research. Roč. 43, č. 20 (2015), s. 9626-9644. ISSN 0305-1048. E-ISSN 1362-4962
R&D Projects: GA ČR(CZ) GAP208/11/1822
Institutional support: RVO:68081707
Keywords : MOLECULAR-DYNAMICS SIMULATIONS * INTRAMOLECULAR DNA QUADRUPLEXES * PARTICLE MESH EWALD
OECD category: Biochemistry and molecular biology
Impact factor: 9.202, year: 2015
Method of publishing: Open access
https://academic.oup.com/nar/article/43/20/9626/1403100
Permanent Link: http://hdl.handle.net/11104/0256640 - 4.0455886 - BFÚ 2016 RIV GB eng J - Journal Article
Islam, B. - Stadlbauer, Petr - Krepl, Miroslav - Koča, J. - Neidle, S. - Haider, S. - Šponer, Jiří
Extended molecular dynamics of a c-kit promoter quadruplex.
Nucleic Acids Research. Roč. 43, č. 18 (2015), s. 8673-8693. ISSN 0305-1048. E-ISSN 1362-4962
R&D Projects: GA ČR(CZ) GAP208/11/1822
Institutional support: RVO:68081707
Keywords : TELOMERIC G-QUADRUPLEX * INTRAMOLECULAR DNA QUADRUPLEXES * GASTROINTESTINAL STROMAL TUMOR
Subject RIV: BO - Biophysics
Impact factor: 9.202, year: 2015
Permanent Link: http://hdl.handle.net/11104/0256495 - 5.0447644 - BFÚ 2016 RIV US eng J - Journal Article
Gresh, N. - Šponer, Judit E. - Devereux, M. - Gkionis, Konstantinos - de Courcy, B. - Piquemal, J.P. - Šponer, Jiří
Stacked and H-Bonded Cytosine Dimers. Analysis of the Intermolecular Interaction Energies by Parallel Quantum Chemistry and Polarizable Molecular Mechanics.
Journal of Physical Chemistry B. Roč. 119, č. 30 (2015), s. 9477-9495. ISSN 1520-6106. E-ISSN 1520-5207
R&D Projects: GA ČR(CZ) GAP208/11/1822
Institutional support: RVO:68081707
Keywords : DENSITY-FUNCTIONAL THEORY * DISTRIBUTED MULTIPOLE ANALYSIS * PERTURBATION-THEORY APPROACH
Subject RIV: BO - Biophysics
Impact factor: 3.187, year: 2015
Permanent Link: http://hdl.handle.net/11104/0249432 - 6.0446226 - BFÚ 2016 RIV GB eng J - Journal Article
Ohnmacht, S.A. - Marchetti, C. - Gunaratnam, M. - Besser, R.J. - Haider, S.M. - Di Vita, G. - Lowe, H.L. - Mellinas-Gomez, M. - Diocou, S. - Robson, M. - Šponer, Jiří … Total 15 authors
A G-quadruplex-binding compound showing anti-tumour activity in an in vivo model for pancreatic cancer.
Scientific Reports. Roč. 5, JUN 2015 (2015). ISSN 2045-2322. E-ISSN 2045-2322
R&D Projects: GA ČR(CZ) GAP208/11/1822; GA MŠMT(CZ) ED1.1.00/02.0068
Institutional support: RVO:68081707
Keywords : NAPHTHALENE DIIMIDE LIGANDS * AMBER FORCE-FIELD * DNA G-QUADRUPLEX
Subject RIV: BO - Biophysics
Impact factor: 5.228, year: 2015
Permanent Link: http://hdl.handle.net/11104/0248219 - 7.0442075 - ÚOCHB 2015 RIV GB eng J - Journal Article
Pasi, M. - Maddocks, J. H. - Beveridge, D. - Bishop, T. C. - Case, D. A. - Cheatham III, T. E. - Dans, P. D. - Jayaram, B. - Lankaš, Filip - Laughton, C. - Mitchell, J. - Osman, R. - Orozco, M. - Pérez, A. - Petkevičiute, D. - Špačková, Naďa - Šponer, Jiří - Zakrzewska, K. - Lavery, R.
mu ABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA.
Nucleic Acids Research. Roč. 42, č. 19 (2014), s. 12272-12283. ISSN 0305-1048. E-ISSN 1362-4962
R&D Projects: GA ČR(CZ) GA14-21893S; GA ČR(CZ) GAP208/11/1822
Grant - others:GA MŠk(CZ) ED1.1.00/02.0068
Program: ED
Institutional support: RVO:61388963 ; RVO:68081707
Keywords : base pair * recognition * conformations
Subject RIV: BO - Biophysics
Impact factor: 9.112, year: 2014
Permanent Link: http://hdl.handle.net/11104/0244974 - 8.0440900 - BFÚ 2015 RIV US eng J - Journal Article
Mlýnský, V. - Banáš, P. - Walter, N.G. - Šponer, Jiří - Otyepka, M.
QM/MM Studies of Hairpin Ribozyme Self-Cleavage Suggest the Feasibility of Multiple Competing Reaction Mechanisms.
Journal of Physical Chemistry B. Roč. 115, č. 47 (2011), s. 13911-13924. ISSN 1520-6106. E-ISSN 1520-5207
R&D Projects: GA ČR(CZ) GAP208/10/2302; GA ČR(CZ) GA203/09/1476; GA ČR(CZ) GAP208/11/1822
Institutional research plan: CEZ:AV0Z50040702
Institutional support: RVO:68081707
Keywords : TRANSITION-STATE STABILIZATION * BASE-PHOSPHATE INTERACTIONS * DENSITY-FUNCTIONAL THEORY
Subject RIV: BO - Biophysics
Impact factor: 3.696, year: 2011
Permanent Link: http://hdl.handle.net/11104/0244011 - 9.0427956 - 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 - 10.0422442 - 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