Search results
- 1.0384773 - BFÚ 2013 RIV GB eng J - Journal Article
Réblová, Kamila - Šponer, Jiří - Lankaš, Filip
Structure and mechanical properties of the ribosomal L1 stalk three-way junction.
Nucleic Acids Research. Roč. 40, č. 13 (2012), s. 6290-6303. ISSN 0305-1048. E-ISSN 1362-4962
R&D Projects: GA ČR(CZ) GA203/09/1476; GA ČR(CZ) GAP208/11/1822; GA ČR(CZ) GAP208/12/1878; GA ČR(CZ) GBP305/12/G034; GA ČR GBP208/12/G016; GA AV ČR(CZ) KJB400040901
Institutional research plan: CEZ:AV0Z50040702; CEZ:AV0Z40550506
Institutional support: RVO:68081707 ; RVO:61388963
Keywords : three-way junction * molecular dynamics * RNA
Subject RIV: BO - Biophysics
Impact factor: 8.278, year: 2012
Permanent Link: http://hdl.handle.net/11104/0214303 - 2.0373420 - 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 - 3.0370696 - 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 - 4.0370399 - 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 - 5.0350506 - BFÚ 2011 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 AV ČR(CZ) IAA400040802; GA AV ČR(CZ) 1QS500040581; GA AV ČR(CZ) KJB400040901; GA ČR(CZ) GD203/09/H046; GA ČR(CZ) GA203/09/1476; GA MŠMT(CZ) LC06030
Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702; CEZ:AV0Z40550506
Keywords : RNA * molecular dynamics * three-way junction
Subject RIV: BO - Biophysics
Impact factor: 7.836, year: 2010
Permanent Link: http://hdl.handle.net/11104/0190497 - 6.0347728 - BFÚ 2011 RIV US eng J - Journal Article
Špačková, Naďa - Réblová, Kamila - Šponer, Jiří
Structural dynamics of the box C/D RNA Kink-Turn and its complex with proteins: The role of the A-minor 0 interaction, long-residency water bridges, and structural ion-binding sites revealed by molecular simulations.
Journal of Physical Chemistry B. Roč. 114, č. 32 (2010), s. 10581-10593. ISSN 1520-6106. E-ISSN 1520-5207
R&D Projects: GA MŠMT(CZ) LC06030; GA AV ČR(CZ) KJB400040901; GA AV ČR(CZ) IAA400040802; GA ČR(CZ) GA203/09/1476
Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702
Keywords : RNA-protein complex * molecular dynamics * kink-turn
Subject RIV: BO - Biophysics
Impact factor: 3.603, year: 2010
Permanent Link: http://hdl.handle.net/11104/0006032 - 7.0345016 - BFÚ 2011 RIV US eng J - Journal Article
Mlýnský, V. - Banáš, P. - Hollas, D. - Réblová, Kamila - Walter, N.G. - Šponer, Jiří - Otyepka, M.
Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme.
Journal of Physical Chemistry B. Roč. 114, č. 19 (2010), s. 6642-6652. 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; GA AV ČR(CZ) IAA400040802; GA AV ČR(CZ) KJB400040901; GA AV ČR(CZ) 1QS500040581
Grant - others:GA MŠk(CZ) LC512
Program: LC
Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702
Keywords : molecular dynamics simulations * hairpin ribozyme
Subject RIV: BO - Biophysics
Impact factor: 3.603, year: 2010
Permanent Link: http://hdl.handle.net/11104/0005937 - 8.0344070 - BFÚ 2011 RIV GB eng J - Journal Article
Réblová, Kamila - Rázga, Filip - Li, W. - Gao, H. - Frank, J. - Šponer, Jiří
Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM.
Nucleic Acids Research. Roč. 38, č. 4 (2010), s. 1325-1340. ISSN 0305-1048. E-ISSN 1362-4962
R&D Projects: GA MŠMT(CZ) LC06030; GA AV ČR(CZ) KJB400040901; GA AV ČR(CZ) 1QS500040581; GA AV ČR(CZ) IAA400040802; GA ČR(CZ) GA203/09/1476
Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702
Keywords : molecular dynamics * Cryo-electron microscopy * RNA
Subject RIV: BO - Biophysics
Impact factor: 7.836, year: 2010
Permanent Link: http://hdl.handle.net/11104/0186380 - 9.0340907 - BFÚ 2010 RIV US eng J - Journal Article
Réblová, Kamila - Střelcová, Z. - Kulhánek, P. - Beššeová, Ivana - Mathews, D.H. - Van Nostrand, K. - Yildirim, I. - Turner, D.H. - Šponer, Jiří
An RNA molecular switch: Intrinsic flexibility of 23S rRNA helices 40 and 68 5’-UAA/5’-GAN internal loops studied by molecular dynamics methods.
Journal of Chemical Theory and Computation. Roč. 6, č. 3 (2010), s. 910-929. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA AV ČR(CZ) 1QS500040581; GA AV ČR(CZ) IAA400040802; GA AV ČR(CZ) KJB400040901
Grant - others:GA MŠk(CZ) LC06030; GA ČR(CZ) GD203/09/H046; GA ČR(CZ) GA203/09/1476
Program: LC; GD; GA
Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702
Keywords : RNA * internal loop * molecular dynamics
Subject RIV: AQ - Safety, Health Protection, Human - Machine
Impact factor: 5.138, year: 2010
Permanent Link: http://hdl.handle.net/11104/0184052 - 10.0333332 - BFÚ 2010 RIV GB eng J - Journal Article
Beššeová, Ivana - Otyepka, Michal - Réblová, Kamila - Šponer, Jiří
Dependence of A-RNA simulations on the choice of the force field and salt strength.
[Závislost simulací A-RNA na volbě silového pole a velikosti iontové síly.]
Physical Chemistry Chemical Physics. Roč. 11, č. 45 (2009), s. 10701-10711. ISSN 1463-9076. E-ISSN 1463-9084
R&D Projects: GA MŠMT(CZ) LC06030; GA AV ČR(CZ) KJB400040901; GA AV ČR(CZ) 1QS500040581; GA AV ČR(CZ) IAA400040802; GA ČR(CZ) GD203/09/H046
Grant - others:GA MŠk(CZ) LC512; GA ČR(CZ) GA203/09/1476
Program: LC; GA
Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702
Keywords : force fileds * RNA * A-form
Subject RIV: BO - Biophysics
Impact factor: 4.116, year: 2009
Permanent Link: http://hdl.handle.net/11104/0178344