Search results
- 1.0379302 - 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 - 2.0379300 - BFÚ 2013 RIV US eng J - Journal Article
Mládek, Arnošt - Šponer, Judit E. - Kulhánek, P. - Lu, X.-J. - Olson, W.K. - Šponer, Jiří
Understanding the sequence preference of recurrent RNA building blocks using quantum chemistry: The intrastrand RNA dinucleotide platform.
Journal of Chemical Theory and Computation. Roč. 8, č. 1 (2012), s. 335-347. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: 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 : RNA dinucleotide platform * quantum-chemical calculation
Subject RIV: BO - Biophysics
Impact factor: 5.389, year: 2012
Permanent Link: http://hdl.handle.net/11104/0210546 - 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 - 4.0376947 - ÚOCHB 2013 RIV US eng J - Journal Article
Rokob, Tibor András - Rulíšek, Lubomír
Curvature Correction for Microiterative Optimizations with QM/MM Electronic Embedding.
Journal of Computational Chemistry. Roč. 33, č. 12 (2012), s. 1197-1206. ISSN 0192-8651. E-ISSN 1096-987X
R&D Projects: GA AV ČR(CZ) IAA400040802
Institutional research plan: CEZ:AV0Z40550506
Keywords : potential-energy surface * quasi-newton matrices * enzymatic-reactions * transition-state search * coordinate transformation problem
Subject RIV: CF - Physical ; Theoretical Chemistry
Impact factor: 3.835, year: 2012
Permanent Link: http://hdl.handle.net/11104/0209226 - 5.0372033 - BFÚ 2012 RIV GB eng J - Journal Article
Reshetnikov, R.V. - Šponer, Jiří - Rassokhina, O.I. - Kopylov, A.M. - Tsvetkov, P.O. - Makarov, A.A. - Golovin, A.V.
Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process.
Nucleic Acids Research. Roč. 39, č. 22 (2011), s. 9789-9802. ISSN 0305-1048. E-ISSN 1362-4962
R&D Projects: GA AV ČR(CZ) IAA400040802; GA ČR(CZ) GA203/09/1476; GA ČR(CZ) GAP208/11/1822; GA MŠMT(CZ) LC06030
Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702
Keywords : QM/MM * quadruplex DNA * molecular dynamics simulation
Subject RIV: BO - Biophysics
Impact factor: 8.026, year: 2011
Permanent Link: http://hdl.handle.net/11104/0205428 - 6.0370696 - BFÚ 2012 RIV US eng J - Journal Article
Réblová, Kamila - Šponer, Judit E. - Špačková, Naďa - Beššeová, Ivana - Šponer, Jiří
A-minor tertiary interactions in RNA kink-turns. Molecular dynamics and quantum chemical analysis.
Journal of Physical Chemistry B. Roč. 115, č. 47 (2011), s. 13897-13910. ISSN 1520-6106. E-ISSN 1520-5207
R&D Projects: GA AV ČR(CZ) KJB400040901; GA AV ČR(CZ) IAA400040802; GA ČR(CZ) GD203/09/H046; GA ČR(CZ) GA203/09/1476; GA ČR(CZ) GAP208/10/2302; GA MŠMT(CZ) LC06030
Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702
Keywords : molecular dynamics * RNA * kink turn
Subject RIV: BO - Biophysics
Impact factor: 3.696, year: 2011
Permanent Link: http://hdl.handle.net/11104/0006793 - 7.0370426 - BFÚ 2012 RIV US eng J - Journal Article
Zgarbová, M. - Otyepka, M. - Šponer, Jiří - Mládek, Arnošt - Banáš, P. - Cheatham III, T.E. - Jurečka, P.
Refinement of the Cornell et al. nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles.
Journal of Chemical Theory and Computation. Roč. 7, č. 9 (2011), s. 2886-2902. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA AV ČR(CZ) IAA400040802; GA ČR(CZ) GD203/09/H046
Grant - others:GA ČR(CZ) GAP208/10/1742; GA ČR(CZ) GPP301/11/P558
Program: GA; GP
Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702
Keywords : molecular-dynamics simulations * density-functional theory * sugar-phosphate backbone
Subject RIV: BO - Biophysics
Impact factor: 5.215, year: 2011
Permanent Link: http://hdl.handle.net/11104/0204230 - 8.0370405 - BFÚ 2012 RIV US eng J - Journal Article
Zgarbová, M. - Jurečka, P. - Banáš, P. - Otyepka, M. - Šponer, Judit E. - Leontis, N.B. - Zirbel, C.L. - Šponer, Jiří
Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of key base-phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations.
Journal of Physical Chemistry A. Roč. 115, č. 41 (2011), s. 11277-11292. ISSN 1089-5639. E-ISSN 1520-5215
R&D Projects: GA AV ČR(CZ) IAA400040802; GA ČR(CZ) GD203/09/H046; GA MŠMT(CZ) LC06030; GA ČR(CZ) GAP208/10/2302; GA ČR(CZ) GA203/09/1476; GA ČR(CZ) GAP208/11/1822
Grant - others:GA ČR(CZ) GAP208/10/1742; GA ČR(CZ) GPP301/11/P558
Program: GA; GP
Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702
Keywords : density-functional theory * large ribosomal-subunit * gaussian-basis sets
Subject RIV: BO - Biophysics
Impact factor: 2.946, year: 2011
Permanent Link: http://hdl.handle.net/11104/0006782 - 9.0370399 - BFÚ 2012 RIV US eng J - Journal Article
Sklenovský, P. - Florová, P. - Banáš, P. - Réblová, Kamila - Lankaš, Filip - Otyepka, M. - Šponer, Jiří
Understanding RNA flexibility using explicit solvent simulations: The ribosomal and group I intron reverse kink-turn motifs.
Journal of Chemical Theory and Computation. Roč. 7, č. 9 (2011), s. 2963-2980. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA ČR(CZ) GD203/09/H046; GA AV ČR(CZ) IAA400040802; GA MŠMT(CZ) LC512; GA AV ČR(CZ) KJB400040901; GA ČR(CZ) GA203/09/1476; GA ČR(CZ) GAP208/11/1822; GA MŠMT(CZ) LC06030
Grant - others:GA ČR(CZ) GPP301/11/P558
Program: GP
Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702; CEZ:AV0Z40550506
Keywords : reverse kink-turn * simulation * flexibility
Subject RIV: BO - Biophysics
Impact factor: 5.215, year: 2011
Permanent Link: http://hdl.handle.net/11104/0204220 - 10.0368851 - BFÚ 2012 RIV US eng J - Journal Article
Vázquez-Mayagoitia, Á. - Horton, S.R. - Sumpter, B.G. - Šponer, Jiří - Šponer, Judit E. - Fuentes-Cabrera, M.
On the stabilization of ribose by silicate minerals.
Astrobiology. Roč. 11, č. 2 (2011), s. 115-121. ISSN 1531-1074. E-ISSN 1557-8070
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) GD203/09/H046
Grant - others:GA MŠk(CZ) LC512
Program: LC
Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702
Keywords : quantum chemistry * prebiotic chemistry * RNA
Subject RIV: BO - Biophysics
Impact factor: 2.150, year: 2011
Permanent Link: http://hdl.handle.net/11104/0203077