Search results
- 1.0576127 - ÚOCHB 2024 RIV US eng J - Journal Article
Biriukov, Denys - Javanainen, Matti
Efficient Simulations of Solvent Asymmetry Across Lipid Membranes Using Flat-Bottom Restraints.
Journal of Chemical Theory and Computation. Roč. 19, č. 18 (2023), s. 6332-6341. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA MŠMT(CZ) LX22NPO5103
Institutional support: RVO:61388963
Keywords : linear constraint solver * particle mesh Ewald * molecular dynamics
OECD category: Physical chemistry
Impact factor: 5.5, year: 2022
Method of publishing: Open access
https://doi.org/10.1021/acs.jctc.3c00614
Permanent Link: https://hdl.handle.net/11104/0345727File Download Size Commentary Version Access 10.1021acs.jctc.3c00614.pdf 0 4.7 MB Publisher’s postprint open-access - 2.0574520 - BFÚ 2024 RIV US eng J - Journal Article
Love, O. - Galindo-Murillo, R. - Zgarbová, M. - Šponer, Jiří - Jurečka, P. - Cheatham III, T. E.
Assessing the Current State of Amber Force Field Modifications for DNA ,2023 Edition.
Journal of Chemical Theory and Computation. Roč. 19, č. 13 (2023), s. 4299-4307. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA ČR(CZ) GA21-23718S
Institutional support: RVO:68081707
Keywords : MOLECULAR-DYNAMICS SIMULATIONS * PARTICLE MESH EWALD * NUCLEIC-ACIDS
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.3c00233
Permanent Link: https://hdl.handle.net/11104/0350087 - 3.0573774 - ÚOCHB 2024 RIV US eng J - Journal Article
Rozsa, Z. B. - Hantal, G. - Szöri, M. - Fábián, Balázs - Jedlovszky, P.
Understanding the Molecular Mechanism of Anesthesia: Effect of General Anesthetics and Structurally Similar Non-Anesthetics on the Properties of Lipid Membranes.
Journal of Physical Chemistry B. Roč. 127, č. 27 (2023), s. 6078-6090. ISSN 1520-6106. E-ISSN 1520-5207
Institutional support: RVO:61388963
Keywords : lateral pressure profiles * particle mesh Ewald * diffusion coefficients
OECD category: Physical chemistry
Impact factor: 3.3, year: 2022
Method of publishing: Limited access
https://doi.org/10.1021/acs.jpcb.3c02976
Permanent Link: https://hdl.handle.net/11104/0344135 - 4.0568445 - ÚOCHB 2024 RIV US eng J - Journal Article
Tempra, Carmelo - Cruces Chamorro, Victor - Jungwirth, Pavel
Effects of Water Deuteration on Thermodynamic and Structural Properties of Proteins and Biomembranes.
Journal of Physical Chemistry B. Roč. 127, č. 5 (2023), s. 1138-1143. ISSN 1520-6106. E-ISSN 1520-5207
R&D Projects: GA ČR(CZ) GX19-26854X
Institutional support: RVO:61388963
Keywords : particle mesh Ewald * heavy water * crystal structure
OECD category: Physical chemistry
Impact factor: 3.3, year: 2022
Method of publishing: Open access
https://doi.org/10.1021/acs.jpcb.2c08270
Permanent Link: https://hdl.handle.net/11104/0339762 - 5.0561693 - ÚOCHB 2023 RIV US eng J - Journal Article
Nguyen, Man Thi Hong - Biriukov, Denys - Tempra, Carmelo - Baxová, Katarína - Martinez-Seara, Hector - Evci, Huseyin - Singh, Vandana - Šachl, Radek - Hof, Martin - Jungwirth, Pavel - Javanainen, Matti - Vazdar, Mario
Ionic Strength and Solution Composition Dictate the Adsorption of Cell-Penetrating Peptides onto Phosphatidylcholine Membranes.
Langmuir. Roč. 38, č. 37 (2022), s. 11284-11295. ISSN 0743-7463
R&D Projects: GA ČR(CZ) GX19-26854X
Institutional support: RVO:61388963 ; RVO:61388955
Keywords : linear constraint solver * particle mesh Ewald * molecular dynamics
OECD category: Physical chemistry
Impact factor: 3.9, year: 2022
Method of publishing: Open access
https://doi.org/10.1021/acs.langmuir.2c01435
Permanent Link: https://hdl.handle.net/11104/0334213File Download Size Commentary Version Access 0561693.pdf 3 14.4 MB open access Publisher’s postprint open-access - 6.0541958 - BFÚ 2022 RIV GB eng J - Journal Article
Jurasek, M. - Kumar, J. - Paclíková, P. - Kumari, A. - Tripsianes, K. - Bryja, Vítězslav - Vácha, R.
Phosphorylation-induced changes in the PDZ domain of Dishevelled 3.
Scientific Reports. Roč. 11, č. 1 (2021), č. článku 1484. ISSN 2045-2322. E-ISSN 2045-2322
Institutional support: RVO:68081707
Keywords : human phosphatase hptp1e * particle mesh ewald * protein interactions * ligand recognition * par-6 pdz * binding
OECD category: Other biological topics
Impact factor: 4.997, year: 2021
Method of publishing: Open access
https://www.nature.com/articles/s41598-020-79398-5
Permanent Link: http://hdl.handle.net/11104/0319474 - 7.0520259 - BFÚ 2020 RIV GB eng J - Journal Article
Harnoš, J. - Canizal, M.C.A. - Jurasek, M. - Kumar, J. - Holler, C. - Schambony, A. - Hanakova, K. - Bernatík, O. - Zdráhal, Z. - Gomoryova, K. - Gybel, T. - Radaszkiewicz, T.W. - Kravec, M. - Trantírek, Lukáš - Ryneš, J. - Dave, Z. - Fernandez-Llamazares, A.I. - Vácha, R. - Tripsianes, K. - Hoffmann, C. - Bryja, Vítězslav
Dishevelled-3 conformation dynamics analyzed by FRET-based biosensors reveals a key role of casein kinase 1.
Nature Communications. Roč. 10, APR 2019 (2019), č. článku 1804. E-ISSN 2041-1723
R&D Projects: GA MŠMT EF15_003/0000477
Institutional support: RVO:68081707
Keywords : particle mesh ewald * beta-catenin * wnt/beta-catenin * dix domain
OECD category: Biochemical research methods
Impact factor: 12.121, year: 2019
Method of publishing: Open access
https://www.nature.com/articles/s41467-019-09651-7.pdf
Permanent Link: http://hdl.handle.net/11104/0304964 - 8.0518355 - BFÚ 2020 RIV GB eng J - Journal Article
Stadlbauer, Petr - Kührová, P. - Vicherek, L. - Banáš, Pavel - Otyepka, Michal - Trantírek, Lukáš - Šponer, Jiří
Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes.
Nucleic Acids Research. Roč. 47, č. 14 (2019), s. 7276-7293. ISSN 0305-1048. E-ISSN 1362-4962
R&D Projects: GA ČR(CZ) GA16-13721S; GA ČR GA17-12075S; GA MŠMT EF15_003/0000477
Institutional support: RVO:68081707
Keywords : telomeric g-quadruplex * amber force-field * monovalent ion parameters * single-molecule fret * particle mesh ewald * nucleic-acids
OECD category: Biochemistry and molecular biology
Impact factor: 11.502, year: 2019
Method of publishing: Open access
https://academic.oup.com/nar/article-pdf/47/14/7276/29185953/gkz610.pdf
Permanent Link: http://hdl.handle.net/11104/0303512 - 9.0517124 - ÚFCH JH 2020 RIV IE eng J - Journal Article
Poojari, C. - Wilkosz, N. - Lira, R. B. - Dimova, R. - Jurkiewicz, Piotr - Petka, R. - Kepczynski, M. - Róg, T.
Behavior of the DPH fluorescence probe in membranes perturbed by drugs.
Chemistry and Physics of Lipids. Roč. 223, SEP 2019 (2019), č. článku 104784. ISSN 0009-3084. E-ISSN 1873-2941
Institutional support: RVO:61388955
Keywords : particle mesh ewald * aa force-field * biophysical properties * model membranes * lipid-membranes * staphylococcus-aureus * unilamellar vesicles * cholesterol * dynamics * dppc * 1,6-diphenyl-1,3,5-hexatriene * Lipid bilayers * Molecular dynamics simulations * Fluorescence anisotropy
OECD category: Physical chemistry
Impact factor: 2.094, year: 2019
Method of publishing: Open access
Permanent Link: http://hdl.handle.net/11104/0302414File Download Size Commentary Version Access 0517124.pdf 0 1.8 MB open access Publisher’s postprint open-access - 10.0504470 - ÚOCHB 2020 RIV US eng J - Journal Article
Jakubec, Dávid - Vondrášek, Jiří
Can All-Atom Molecular Dynamics Simulations Quantitatively Describe Homeodomain-DNA Binding Equilibria?
Journal of Chemical Theory and Computation. Roč. 15, č. 4 (2019), s. 2635-2648. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA MŠMT(CZ) EF16_019/0000729; GA MŠMT(CZ) LM2015047
Institutional support: RVO:61388963
Keywords : free energy calculations * particle mesh Ewald * force field
OECD category: Physical chemistry
Impact factor: 5.011, year: 2019
Method of publishing: Limited access
https://pubs.acs.org/doi/10.1021/acs.jctc.8b01144
Permanent Link: http://hdl.handle.net/11104/0296094