Search results

  1. 1.
    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
     
     
  2. 2.
    0569227 - BFÚ 2023 RIV US eng J - Journal Article
    Pokorná, Pavlína - Krepl, Miroslav - Campagne, S. - Šponer, Jiří
    Conformational Heterogeneity of RNA Stem-Loop Hairpins Bound to FUS-RNA Recognition Motif with Disordered RGG Tail Revealed by Unbiased Molecular Dynamics Simulations.
    Journal of Physical Chemistry B. Roč. 126, č. 45 (2022), s. 9207-9221. ISSN 1520-6106. E-ISSN 1520-5207
    R&D Projects: GA ČR(CZ) GA20-16554S; GA MŠMT EF15_003/0000477
    Institutional support: RVO:68081707
    Keywords : FORCE-FIELD * NUCLEIC-ACIDS * AMBER * BACKBONE * BINDING
    OECD category: Clinical neurology
    Impact factor: 3.3, year: 2022
    Method of publishing: Open access
    https://pubs.acs.org/doi/10.1021/acs.jpcb.2c06168
    Permanent Link: https://hdl.handle.net/11104/0340609
     
     
  3. 3.
    0557417 - BFÚ 2023 RIV US eng J - Journal Article
    Mlýnský, Vojtech - Janecek, M. - Kührová, Petra - Frohlking, T. - Otyepka, M. - Bussi, G. - Banáš, Pavel - Šponer, Jiří
    Toward Convergence in Folding Simulations of RNA Tetraloops : Comparison of Enhanced Sampling Techniques and Effects of Force Field Modifications br.
    Journal of Chemical Theory and Computation. Roč. 18, č. 4 (2022), s. 2642-2656. ISSN 1549-9618. E-ISSN 1549-9626
    R&D Projects: GA MŠMT EF15_003/0000477; GA ČR(CZ) GA20-16554S
    Institutional support: RVO:68081707
    Keywords : free-energy landscape * molecular-dynamics * replica-exchange * tertiary interactions * parameters * hairpins
    OECD category: Organic chemistry
    Impact factor: 5.5, year: 2022
    Method of publishing: Limited access
    https://pubs.acs.org/doi/10.1021/acs.jctc.1c01222
    Permanent Link: https://hdl.handle.net/11104/0339585
     
     
  4. 4.
    0554903 - BFÚ 2022 RIV US eng J - Journal Article
    Janeček, Michal - Kührová, P. - Mlýnský, Vojtech - Otyepka, Michal - Šponer, Jiří - Banáš, Pavel
    W-RESP: Well-Restrained Electrostatic Potential-Derived Charges. Revisiting the Charge Derivation Model.
    Journal of Chemical Theory and Computation. Roč. 17, č. 6 (2021), s. 3495-3509. ISSN 1549-9618. E-ISSN 1549-9626
    R&D Projects: GA ČR(CZ) GA20-16554S
    Institutional support: RVO:68081707
    Keywords : correlated molecular calculations * gaussian-basis sets * density-functional theory * partial atomic charges * force-field * ab-initio
    OECD category: Physical chemistry
    Impact factor: 6.578, year: 2021
    Method of publishing: Open access
    https://pubs.acs.org/doi/10.1021/acs.jctc.0c00976
    Permanent Link: http://hdl.handle.net/11104/0329517
     
     
  5. 5.
    0554790 - BFÚ 2022 RIV US eng J - Journal Article
    Krepl, Miroslav - Damberger, F.F. - von Schroetter, C. - Theler, D. - Pokorná, Pavlína - Allain, F.H.T. - Šponer, Jiří
    Recognition of N6-Methyladenosine by the YTHDC1 YTH Domain Studied by Molecular Dynamics and NMR Spectroscopy: The Role of Hydration.
    Journal of Physical Chemistry B. Roč. 125, č. 28 (2021), s. 7691-7705. ISSN 1520-6106. E-ISSN 1520-5207
    R&D Projects: GA ČR(CZ) GA20-16554S
    Institutional support: RVO:68081707
    Keywords : force-field * structural basis * ring-current * m(6)a rna * parameters
    OECD category: Analytical chemistry
    Impact factor: 3.466, year: 2021
    Method of publishing: Open access
    https://pubs.acs.org/doi/10.1021/acs.jpcb.1c03541
    Permanent Link: http://hdl.handle.net/11104/0329442
     
     
  6. 6.
    0553643 - BFÚ 2022 RIV US eng J - Journal Article
    Krepl, Miroslav - Dendooven, T. - Luisi, B. - Šponer, Jiří
    MD simulations reveal the basis for dynamic assembly of Hfq-RNA complexes.
    Journal of Biological Chemistry. Roč. 296, JAN-JUN 2021 (2021), č. článku 100656. ISSN 0021-9258. E-ISSN 1083-351X
    R&D Projects: GA ČR(CZ) GA20-16554S
    Institutional support: RVO:68081707
    Keywords : molecular-dynamics * side-chain
    OECD category: Biochemistry and molecular biology
    Impact factor: 5.485, year: 2021
    Method of publishing: Open access
    https://www.jbc.org/action/showPdf?pii=S0021-9258%2821%2900443-9
    Permanent Link: http://hdl.handle.net/11104/0328391
     
     
  7. 7.
    0541951 - BFÚ 2022 RIV GB eng J - Journal Article
    Clery, A. - Krepl, Miroslav - Nguyen, C. K. X. - Moursy, A. - Jorjani, H. - Katsantoni, M. - Okoniewski, M. - Mittal, N. - Zavolan, M. - Šponer, Jiří - Allain, F.H.T.
    Structure of SRSF1 RRM1 bound to RNA reveals an unexpected bimodal mode of interaction and explains its involvement in SMN1 exon7 splicing.
    Nature Communications. Roč. 12, č. 1 (2021), č. článku 428. E-ISSN 2041-1723
    R&D Projects: GA ČR(CZ) GA20-16554S
    Institutional support: RVO:68081707
    Keywords : pre-messenger-rna * spinal muscular-atrophy * protein-protein interactions * nmr structure determination * sr protein * recognition motifs
    OECD category: Physical chemistry
    Impact factor: 17.694, year: 2021
    Method of publishing: Open access
    https://www.nature.com/articles/s41467-020-20481-w
    Permanent Link: http://hdl.handle.net/11104/0319465
     
     
  8. 8.
    0541887 - BFÚ 2022 RIV US eng J - Journal Article
    Zhang, Z. - Vogele, J. - Mráziková, Klaudia - Kruse, Holger - Cang, X. - Woehnert, J. - Krepl, Miroslav - Šponer, Jiří
    Phosphorothioate Substitutions in RNA Structure Studied by Molecular Dynamics Simulations, QM/MM Calculations, and NMR Experiments.
    Journal of Physical Chemistry B. Roč. 125, č. 3 (2021), s. 825-840. ISSN 1520-6106. E-ISSN 1520-5207
    R&D Projects: GA ČR(CZ) GA20-16554S; GA MŠMT EF15_003/0000477
    Institutional support: RVO:68081707
    Keywords : RNA Structure * Molecular Dynamics Simulations * QM/MM Calculations * NMR Experiments
    OECD category: Physical chemistry
    Impact factor: 3.466, year: 2021
    Method of publishing: Limited access
    https://pubs.acs.org/doi/10.1021/acs.jpcb.0c10192
    Permanent Link: http://hdl.handle.net/11104/0319383
     
     
  9. 9.
    0540054 - BFÚ 2021 RIV US eng J - Journal Article
    Mráziková, Klaudia - Mlýnský, Vojtech - Kührová, P. - Pokorná, Pavlína - Kruse, Holger - Krepl, Miroslav - Otyepka, Michal - Banáš, Pavel - Šponer, Jiří
    UUCG RNA Tetraloop as a Formidable Force-Field Challenge for MD Simulations.
    Journal of Chemical Theory and Computation. Roč. 16, č. 12 (2020), s. 7601-7617. ISSN 1549-9618. E-ISSN 1549-9626
    R&D Projects: GA ČR(CZ) GA20-16554S; GA MŠMT EF15_003/0000477
    Institutional support: RVO:68081707
    Keywords : UUCG RNA Tetraloop * Force-Field * MD Simulations
    OECD category: Atomic, molecular and chemical physics (physics of atoms and molecules including collision, interaction with radiation, magnetic resonances, Mössbauer effect)
    Impact factor: 6.006, year: 2020
    Method of publishing: Limited access
    https://pubs.acs.org/doi/10.1021/acs.jctc.0c00801
    Permanent Link: http://hdl.handle.net/11104/0317722
     
     
  10. 10.
    0539743 - BFÚ 2021 RIV US eng J - Journal Article
    Mlýnský, Vojtech - Kührová, P. - Kuhr, T. - Otyepka, Michal - Bussi, G. - Banáš, Pavel - Šponer, Jiří
    Fine-Tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides.
    Journal of Chemical Theory and Computation. Roč. 16, č. 6 (2020), s. 3936-3946. ISSN 1549-9618. E-ISSN 1549-9626
    R&D Projects: GA ČR(CZ) GA20-16554S
    Institutional support: RVO:68081707
    Keywords : molecular-dynamics simulations * monovalent ion parameters * replica exchange * stacking * energies * nmr
    OECD category: Atomic, molecular and chemical physics (physics of atoms and molecules including collision, interaction with radiation, magnetic resonances, Mössbauer effect)
    Impact factor: 6.006, year: 2020
    Method of publishing: Limited access
    https://pubs.acs.org/doi/10.1021/acs.jctc.0c00228
    Permanent Link: http://hdl.handle.net/11104/0317442
     
     


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