Search results
- 1.0318555 - BFÚ 2009 RIV US eng J - Journal Article
Vokáčová, Zuzana - Šponer, Jiří - Šponer, Judit E. - Sychrovský, Vladimír
Theoretical study of the scalar coupling constants across the noncovalent contacts in RNA base pairs: The cis- and trans-Watson-Crick/sugar edge base pair family.
[Teoretická studie skalárních coupling konstant v nekovalentních kontaktech RNA párů bází: cis a trans páry bází rodiny Watson-Crick/sugar edge.]
Journal of Physical Chemistry B. Roč. 111, č. 36 (2007), s. 10813-10824. ISSN 1520-6106. E-ISSN 1520-5207
R&D Projects: GA ČR(CZ) GA203/05/0388; GA ČR(CZ) GA203/06/0420; GA AV ČR(CZ) IAA400550701; GA MŠMT(CZ) LC06030
Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702; CEZ:AV0Z40550506
Keywords : RNA base pairs * NMR spin-spin coupling constant * theoretical calculations
Subject RIV: BO - Biophysics
Impact factor: 4.086, year: 2007
Permanent Link: http://hdl.handle.net/11104/0004969 - 2.0313216 - BFÚ 2009 RIV US eng J - Journal Article
Kosenkov, D. - Gorb, L. - Shishkin, O.V. - Šponer, Jiří - Leszczynski, J.
Tautomeric equilibrium, stability, and hydrogen bonding in 2'-deoxyguanosine monophosphate complexed with Mg2+.
[Tautomerní rovnováha, stabilita a vodíkové vazby v 2'-deoxyguanosine monofosfátu v komplexu s Mg2+.]
Journal of Physical Chemistry B. Roč. 112, č. 1 (2008), s. 150-157. ISSN 1520-6106. E-ISSN 1520-5207
R&D Projects: GA ČR(CZ) GA203/05/0009; GA ČR(CZ) GA203/05/0388; GA MŠMT(CZ) LC06030; GA AV ČR(CZ) 1QS500040581
Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702
Keywords : quantum chemistry * nucleic acids
Subject RIV: AQ - Safety, Health Protection, Human - Machine
Impact factor: 4.189, year: 2008
Permanent Link: http://hdl.handle.net/11104/0004772 - 3.0093336 - BFÚ 2008 RIV US eng J - Journal Article
Réblová, Kamila - Fadrná, E. - Sarzynska, J. - Kulinski, T. - Kulhánek, P. - Ennifar, E. - Koča, J. - Šponer, Jiří
Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics.
[Konformace volných bází v HIV-1 RNA DIS kissing loop komplexech studovaných molekulovou dynamikou.]
Biophysical Journal. Roč. 93, č. 11 (2007), s. 3932-3949. ISSN 0006-3495. E-ISSN 1542-0086
R&D Projects: GA MŠMT(CZ) LC06030; GA ČR(CZ) GA203/05/0009; GA ČR(CZ) GA203/05/0388; GA AV ČR(CZ) 1QS500040581
Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702
Keywords : molecular dynamics * RNA * virus
Subject RIV: BO - Biophysics
Impact factor: 4.627, year: 2007
Permanent Link: http://hdl.handle.net/11104/0153404 - 4.0089963 - BFÚ 2008 RIV US eng J - Journal Article
Šponer, Jiří - Špačková, Naďa
Molecular dynamics simulations and their application to four-stranded DNA.
[Molekulově dynamické simulace a jejich aplikace na čtyřřetězcové DNA.]
Methods. Roč. 43, - (2007), s. 278-290. ISSN 1046-2023. E-ISSN 1095-9130
R&D Projects: GA ČR(CZ) GA203/05/0009; GA ČR(CZ) GA203/05/0388; GA AV ČR(CZ) 1QS500040581; GA AV ČR(CZ) IAA400550701
Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702
Keywords : computational modeling * failure * limitations
Subject RIV: BO - Biophysics
Impact factor: 3.667, year: 2007
Permanent Link: http://hdl.handle.net/11104/0151001 - 5.0089954 - BFÚ 2008 RIV US eng J - Journal Article
Šponer, Judit E. - Réblová, Kamila - Mokdad, A. - Sychrovský, Vladimír - Leszczynski, J. - Šponer, Jiří
Leading RNA tertiary interactions: Structures, energies, and water insertion of a-minor and P-interactions. A quantum chemical view.
[Hlavní RNA terciární interakce: Struktura, energetika a inzerce v A-minor a P-interakcích. Kvantově chemický pohled.]
Journal of Physical Chemistry B. Roč. 111, č. 30 (2007), s. 9153-9164. ISSN 1520-6106. E-ISSN 1520-5207
R&D Projects: GA ČR(CZ) GA203/05/0009; GA ČR(CZ) GA203/05/0388; GA AV ČR(CZ) IAA400550701; GA MŠMT(CZ) LC512
Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702; CEZ:AV0Z40550506
Keywords : P-motif * A-minor motif * QM
Subject RIV: BO - Biophysics
Impact factor: 4.086, year: 2007
Permanent Link: http://hdl.handle.net/11104/0004265 - 6.0089118 - BC 2008 RIV US eng J - Journal Article
Trantírek, Lukáš - Caha, E. - Kadeřávek, P. - Fiala, R.
NMR (13)C-relaxation study of base and sugar dynamics in GCAA RNA hairpin tetraloop.
[Studium dynamiky bazí a cukrů ve smyčce GCAA pomocí 13C-relaxace NMR.]
Journal of Biomolecular Structure & Dynamics. Roč. 25, č. 3 (2007), s. 243-252. ISSN 0739-1102
R&D Projects: GA ČR GA203/05/0388; GA MŠMT(CZ) LC06030
Grant - others:GA ČR(CZ) GA203/99/0311; EU FSG-V-RNA, 6th Framework Program EU
Institutional research plan: CEZ:AV0Z60220518
Source of funding: R - Framework programmes of European Commission
Keywords : RNA * GNRA * NMR * GCAA * relaxation * dynamics * hairpin * tetraloop
Subject RIV: CE - Biochemistry
Impact factor: 1.413, year: 2007
Permanent Link: http://hdl.handle.net/11104/0150447 - 7.0087360 - ÚOCHB 2008 RIV US eng J - Journal Article
Vokáčová, Zuzana - Šponer, Jiří - Šponer, Judit E. - Sychrovský, Vladimír
Theoretical Study of the Scalar Coupling Constants across the Noncovalent Contacts in RNA Base Pairs: The cis- and trans-Watson-Crick/Sugar Edge Base Pair Family.
[Teoretická studie skalárních kaplingů v nekovalentních vazbách u párů bazí RNA: Cis- a Trans-Watson-Crick/Sugar Edge skupina páru bazí.]
Journal of Physical Chemistry B. Roč. 111, č. 36 (2007), s. 10813-10824. ISSN 1520-6106. E-ISSN 1520-5207
R&D Projects: GA ČR GA203/05/0388; GA ČR GA203/06/0420; GA AV ČR IAA400550701; GA MŠMT(CZ) LC06030
Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z50040507
Keywords : NMR * hydrogen bond * RNA
Subject RIV: CF - Physical ; Theoretical Chemistry
Impact factor: 4.086, year: 2007
Permanent Link: http://hdl.handle.net/11104/0004186 - 8.0087248 - BFÚ 2008 RIV GB eng J - Journal Article
Rázga, Filip - Koča, J. - Mokdad, A. - Šponer, Jiří
Elastic properties of ribosomal RNA building blocks: Molecular dynamics of the GTPase-associated center rRNA.
[Elastické vlastnosti stavebních bloků rRNA: molekulární dynamika GTPase-associated center rRNA.]
Nucleic Acids Research. Roč. 35, č. 12 (2007), s. 4007-4017. ISSN 0305-1048. E-ISSN 1362-4962
R&D Projects: GA MŠMT(CZ) LC06030; GA ČR(CZ) GA203/05/0388; GA ČR(CZ) GA203/05/0009; GA AV ČR(CZ) 1QS500040581
Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702
Keywords : molecular dynamics * RNA building blocks * ribosome
Subject RIV: BO - Biophysics
Impact factor: 6.954, year: 2007
Permanent Link: http://hdl.handle.net/11104/0149145 - 9.0081998 - BFÚ 2007 RIV GB eng J - Journal Article
Šefčíková, J. - Krasovská, Maryna V. - Šponer, Jiří - Walter, N.G.
The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis.
[Genomický HDV ribozym využívá předtím nepovšimnutý U-turn motiv na rychlou site-specific katalýzu.]
Nucleic Acids Research. Roč. 35, č. 6 (2007), s. 1933-1946. ISSN 0305-1048. E-ISSN 1362-4962
R&D Projects: GA ČR(CZ) GA203/05/0388; GA ČR(CZ) GA203/05/0009; GA AV ČR(CZ) 1QS500040581; GA AV ČR(CZ) IAA400550701; GA MŠMT(CZ) LC512
Institutional research plan: CEZ:AV0Z50040702; CEZ:AV0Z40550506
Keywords : hepatitis delta virus * molecular dynamics * self-cleavage
Subject RIV: BO - Biophysics
Impact factor: 6.954, year: 2007
Permanent Link: http://hdl.handle.net/11104/0145700 - 10.0081633 - BFÚ 2007 RIV US eng J - Journal Article
Šefčíková, J. - Krasovská, Maryna V. - Špačková, Naďa - Šponer, Jiří - Walter, N.G.
Impact of an extruded nucleotide on cleavage activity and dynamic catalytic core conformation of the hepatitis delta virus ribozyme.
[Vliv vytěsněného nukleotidu na aktivitu štěpení a konformační dynamiku katalytického jádra hepatitis delta virus ribozymu.]
Biopolymers. Roč. 85, 5-6 (2007), s. 392-406. ISSN 0006-3525. E-ISSN 1097-0282
R&D Projects: GA ČR(CZ) GA203/05/0388; GA ČR(CZ) GA203/05/0009; GA AV ČR(CZ) 1QS500040581; GA MŠMT(CZ) LC512
Institutional research plan: CEZ:AV0Z50040702
Keywords : conformational dynamics * hepatitis delta virus * molecular dynamics
Subject RIV: BO - Biophysics
Impact factor: 2.389, year: 2007
Permanent Link: http://hdl.handle.net/11104/0145436