Search results
- 1.0583260 - BFÚ 2024 RIV US eng J - Journal Article
Mlýnský, Vojtech - Kührová, Petra - Stadlbauer, Petr - Krepl, Miroslav - Otyepka, M. - Banáš, Pavel - Šponer, Jiří
Simple Adjustment of Intranucleotide Base-Phosphate Interaction in the OL3 AMBER Force Field Improves RNA Simulations.
Journal of Chemical Theory and Computation. Roč. 19, č. 22 (2023), s. 8423-8433. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA ČR(CZ) GA23-05639S
Institutional support: RVO:68081707
Keywords : molecular-dynamics simulations * replica exchange * parameters * tetraloops * uucg * nmr * resolution
OECD category: Atomic, molecular and chemical physics (physics of atoms and molecules including collision, interaction with radiation, magnetic resonances, Mössbauer effect)
Impact factor: 5.5, year: 2022
Method of publishing: Open access
https://pubs.acs.org/doi/10.1021/acs.jctc.3c00990
Permanent Link: https://hdl.handle.net/11104/0351262 - 2.0574950 - BFÚ 2024 RIV US eng J - Journal Article
Qiu, D. - Cheng, M. - Stadlbauer, Petr - Chen, J. - Langer, M. - Zhang, X. - Gao, Q. - Ju, H. - Šponer, Jiří - Mergny, Jean-Louis - Monchaud, D. - Zhou, J.
Topology of DNA G-Quadruplexes Can Be Harnessed in Holliday Junction-Based DNA Suprastructures to Control and Optimize Their Biocatalytic Properties.
ACS Catalysis. Roč. 13, č. 16 (2023), s. 10722-10733. ISSN 2155-5435. E-ISSN 2155-5435
R&D Projects: GA MŠMT EF15_003/0000477; GA ČR(CZ) GA21-23718S
Institutional support: RVO:68081707
Keywords : G-quadruplex * DNAzyme * Holliday junction * molecular dynamics simulations * catalytic mechanism
OECD category: Physical chemistry
Impact factor: 12.9, year: 2022
Method of publishing: Open access
https://pubs.acs.org/doi/10.1021/acscatal.3c02818
Permanent Link: https://hdl.handle.net/11104/0349523 - 3.0574511 - BFÚ 2024 RIV US eng J - Journal Article
Stadlbauer, Petr - Mlýnský, Vojtech - Krepl, Miroslav - Šponer, Jiří
Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations.
Journal of Chemical Information and Modeling. Roč. 63, č. 15 (2023), s. 4716-4731. ISSN 1549-9596. E-ISSN 1549-960X
R&D Projects: GA ČR(CZ) GA21-23718S
Institutional support: RVO:68081707
Keywords : TELOMERIC G-QUADRUPLEX * DNA G-QUADRUPLEXES * MOLECULAR-DYNAMICS
OECD category: Biochemistry and molecular biology
Impact factor: 5.6, year: 2022
Method of publishing: Open access
https://pubs.acs.org/doi/10.1021/acs.jcim.3c00171
Permanent Link: https://hdl.handle.net/11104/0350040 - 4.0569826 - BFÚ 2023 RIV GB eng J - Journal Article
Krepl, Miroslav - Pokorná, Pavlína - Mlýnský, Vojtech - Stadlbauer, Petr - Šponer, Jiří
Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field.
Nucleic Acids Research. Roč. 50, č. 21 (2022), s. 12480-12496. ISSN 0305-1048. E-ISSN 1362-4962
R&D Projects: GA ČR(CZ) GA20-16554S; GA MŠMT EF15_003/0000477
Institutional support: RVO:68081707
Keywords : MOLECULAR-DYNAMICS SIMULATIONS * REPLICA EXCHANGE * RECOGNITION MOTIFS
OECD category: Biochemistry and molecular biology
Impact factor: 14.9, year: 2022
Method of publishing: Limited access
https://academic.oup.com/nar/article/50/21/12480/6858795?login=true
Permanent Link: https://hdl.handle.net/11104/0341159 - 5.0563710 - BFÚ 2023 RIV CN eng J - Journal Article
Chen, J. - Cheng, M. - Stadlbauer, Petr - Šponer, Jiří - Mergny, Jean-Louis - Ju, H. - Zhou, J.
Exploring Sequence Space to Design Controllable G-Quadruplex Topology Switches.
CCS CHEMISTRY. Roč. 4, č. 9 (2022), s. 3036-3050. E-ISSN 2096-5745
R&D Projects: GA ČR(CZ) GA21-23718S; GA MŠMT EF15_003/0000477
Institutional support: RVO:68081707
Keywords : G-quadruplex * G-quadruplex topology * G-switch * sequence composition * structural versatility
OECD category: Biochemistry and molecular biology
Impact factor: 11.2, year: 2022
Method of publishing: Open access
https://www.chinesechemsoc.org/doi/10.31635/ccschem.021.202101357
Permanent Link: https://hdl.handle.net/11104/0339366 - 6.0555379 - BFÚ 2022 RIV GB eng J - Journal Article
Szabla, R. - Zdrowowicz, M. - Spisz, P. - Green, N. - Stadlbauer, Petr - Kruse, Holger - Šponer, Jiří - Rak, J.
2,6-diaminopurine promotes repair of DNA lesions under prebiotic conditions.
Nature Communications. Roč. 12, č. 1 (2021), č. článku 3018. E-ISSN 2041-1723
R&D Projects: GA ČR(CZ) GA21-23718S; GA MŠMT EF15_003/0000477
Institutional support: RVO:68081707
Keywords : excited-state dynamics * cyclobutane pyrimidine dimers * charge-transfer states * amber force-field * molecular-dynamics
OECD category: Biochemistry and molecular biology
Impact factor: 17.694, year: 2021
Method of publishing: Open access
https://www.nature.com/articles/s41467-021-23300-y.pdf
Permanent Link: http://hdl.handle.net/11104/0329897 - 7.0554847 - BFÚ 2022 RIV DE eng J - Journal Article
Kejnovská, Iva - Stadlbauer, Petr - Trantírek, L. - Renčiuk, Daniel - Gajarský, M. - Krafčík, D. - Palacký, Jan - Bednářová, Klára - Šponer, Jiří - Mergny, Jean-Louis - Vorlíčková, Michaela
G-Quadruplex Formation by DNA Sequences Deficient in Guanines: Two Tetrad Parallel Quadruplexes Do Not Fold Intramolecularly.
Chemistry - A European Journal. Roč. 27, č. 47 (2021), s. 12115-12125. ISSN 0947-6539. E-ISSN 1521-3765
R&D Projects: GA ČR(CZ) GA19-17063S; GA ČR(CZ) GA20-20229S; GA ČR(CZ) GA21-23718S; GA MŠMT EF15_003/0000477
Institutional support: RVO:68081707
Keywords : amber force-field * human telomere * molecular-dynamics * nucleic-acids * k+ solution * crystal-structure
OECD category: Biochemistry and molecular biology
Impact factor: 5.020, year: 2021
Method of publishing: Limited access
https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/chem.202100895
Permanent Link: http://hdl.handle.net/11104/0329475 - 8.0554476 - BFÚ 2022 RIV GB eng J - Journal Article
Chen, J. - Cheng, M. - Salgado, G.F. - Stadlbauer, Petr - Zhang, X. - Amrane, S. - Guédin, A. - He, F. - Šponer, Judit E. - Ju, H. - Mergny, Jean-Louis - Zhou, J.
The beginning and the end: flanking nucleotides induce a parallel G-quadruplex topology.
Nucleic Acids Research. Roč. 49, č. 16 (2021), s. 9548-9559. ISSN 0305-1048. E-ISSN 1362-4962
R&D Projects: GA ČR(CZ) GA21-23718S; GA MŠMT EF15_003/0000477
Institutional support: RVO:68081707
Keywords : loop-length * k+ solution * dna * stability * sequence
OECD category: Biochemistry and molecular biology
Impact factor: 19.160, year: 2021
Method of publishing: Open access
https://academic.oup.com/nar/article/49/16/9548/6348194
Permanent Link: http://hdl.handle.net/11104/0329188 - 9.0551530 - BFÚ 2023 RIV GB eng J - Journal Article
Asha, H. - Stadlbauer, Petr - Martinez-Fernandez, L. - Banáš, Pavel - Šponer, Jiří - Improta, R. - Esposito, L.
Early steps of oxidative damage in DNA quadruplexes are position-dependent: Quantum mechanical and molecular dynamics analysis of human telomeric sequence containing ionized guanine.
International Journal of Biological Macromolecules. Roč. 194, JAN 1 2022 (2022), s. 882-894. ISSN 0141-8130. E-ISSN 1879-0003
R&D Projects: GA ČR(CZ) GA21-23718S; GA MŠMT EF15_003/0000477
Institutional support: RVO:68081707
Keywords : monovalent ion parameters * radical-cation transport * one-electron oxidation * circular-dichroism * crystal-structure * laser photolysis * charge-transport
OECD category: Biochemistry and molecular biology
Impact factor: 8.2, year: 2022
Method of publishing: Open access
https://www.sciencedirect.com/science/article/pii/S0141813021025484?via%3Dihub
Permanent Link: https://hdl.handle.net/11104/0336909 - 10.0542802 - BFÚ 2022 RIV GB eng J - Journal Article
Zivkovic, M.L. - Gajarský, M. - Bekova, K. - Stadlbauer, Petr - Vicherek, L. - Petrová, Magdalena - Fiala, R. - Rosenberg, Ivan - Šponer, Jiří - Plavec, J. - Trantírek, L.
Insight into formation propensity of pseudocircular DNA G-hairpins.
Nucleic Acids Research. Roč. 49, č. 4 (2021), s. 2317-2332. ISSN 0305-1048. E-ISSN 1362-4962
R&D Projects: GA ČR(CZ) GA17-12703S; GA MŠMT EF15_003/0000477
Institutional support: RVO:68081707 ; RVO:61388963
Keywords : molecular-dynamics simulations * g-quadruplex structure * amber force-field * g-triplex * folding pathways
OECD category: Biochemistry and molecular biology; Biochemistry and molecular biology (UOCHB-X)
Impact factor: 19.160, year: 2021
Method of publishing: Open access
https://academic.oup.com/nar/article/49/4/2317/6125665
Permanent Link: http://hdl.handle.net/11104/0320148