Search results
- 1.0578251 - ÚOCHB 2025 RIV NL eng J - Journal Article
Saija, M. C. - Melcrová, A. - Pajerski, W. - Schachter, Itay - Javanainen, Matti - Cebecauer, M. - Cwiklik, Lukasz
Palmitoylation modifies transmembrane adaptor protein PAG for ordered lipid environment: A molecular dynamics simulation study.
Biophysical Chemistry. Roč. 304, January (2024), č. článku 107124. ISSN 0301-4622. E-ISSN 1873-4200
R&D Projects: GA ČR(CZ) GX19-26854X
Institutional support: RVO:61388963
Keywords : PAG * membranes * palmitoylation * lipid membrane phases * MD simulations
Impact factor: 3.8, year: 2022
Method of publishing: Limited access
https://doi.org/10.1016/j.bpc.2023.107124
Permanent Link: https://hdl.handle.net/11104/0347277 - 2.0575728 - ÚT 2024 IT eng A - Abstract
Aminian, Ali - Vinš, Václav
MD simulations and excess entropy scaling for the transport properties of dense HFEs.
22nd EUROPEAN CONFERENCE ON THERMOPHYSICAL PROPERTIES. Venice, 2023. s. 168-168. ISBN 9791221042207.
[European Conference on Thermophysical Properties /22./. 10.09.2023-13.09.2023, Venice]
R&D Projects: GA ČR(CZ) GA22-03380S
Institutional support: RVO:61388998
Keywords : transport properties * refrigerants * MD simulations * excess entropy scaling
OECD category: Thermodynamics
https://www.ectp2023.eu/book-of-abstracts
Permanent Link: https://hdl.handle.net/11104/0349489 - 3.0574517 - BFÚ 2024 RIV US eng J - Journal Article
Voegele, J. - Duchardt-Ferner, E. - Kruse, Holger - Zhang, Zhengyue - Šponer, Jiří - Krepl, Miroslav - Woehnert, J.
Structural and dynamic effects of pseudouridine modifications on noncanonical interactions in RNA.
RNA. Roč. 29, č. 6 (2023), s. 790-807. ISSN 1355-8382. E-ISSN 1469-9001
R&D Projects: GA ČR(CZ) GA23-05639S
Institutional support: RVO:68081707
Keywords : pseudouridine * RNA structure * U-turn * U base pair * nmr * MD simulations
OECD category: Biochemistry and molecular biology
Impact factor: 4.5, year: 2022
Method of publishing: Limited access
https://rnajournal.cshlp.org/content/29/6/790
Permanent Link: https://hdl.handle.net/11104/0350076 - 4.0569260 - BFÚ 2023 RIV DE eng J - Journal Article
Paloncyova, M. - Pykal, M. - Kührová, P. - Banáš, P. - Šponer, Jiří - Otyepka, M.
Computer Aided Development of Nucleic Acid Applications in Nanotechnologies.
Small. Roč. 18, č. 49 (2022). ISSN 1613-6810. E-ISSN 1613-6829
R&D Projects: GA ČR(CZ) GA21-23718S
Institutional support: RVO:68081707
Keywords : biosensors * force fields * lipid nanoparticles * MD simulations * nucleic acids * nucleic acid templated assemblies
OECD category: Coating and films
Impact factor: 13.3, year: 2022
Method of publishing: Limited access
https://onlinelibrary.wiley.com/doi/10.1002/smll.202204408
Permanent Link: https://hdl.handle.net/11104/0340647 - 5.0554617 - ÚMG 2022 RIV GB eng J - Journal Article
Glatzová, Daniela - Mavila, H. - Saija, M.C. - Chum, T. - Cwiklik, L. - Brdička, Tomáš - Cebecauer, M.
The role of prolines and glycine in the transmembrane domain of LAT.
FEBS Journal. Roč. 288, č. 13 (2021), s. 4039-4052. ISSN 1742-464X. E-ISSN 1742-4658
R&D Projects: GA MŠMT(CZ) LM2015062; GA MŠMT(CZ) EF16_013/0001775; GA MŠMT LO1419
Research Infrastructure: Czech-BioImaging - 90062
Institutional support: RVO:68378050
Keywords : lat * MD simulations * microscopy * T cells * transmembrane domain
OECD category: Biochemistry and molecular biology
Impact factor: 5.622, year: 2021
Method of publishing: Limited access
https://febs.onlinelibrary.wiley.com/doi/10.1111/febs.15713
Permanent Link: http://hdl.handle.net/11104/0329312 - 6.0553493 - MBÚ 2023 RIV CH eng J - Journal Article
Zara, Zeenat - Mishra, Deepti - Pandey, Saurabh Kumar - Cséfalvay, Eva - Fadaei, Fatemeh - Minofar, Babak - Řeha, David
Surface Interaction of Ionic Liquids: Stabilization of Polyethylene Terephthalate-Degrading Enzymes in Solution.
Molecules. Roč. 27, č. 1 (2022), č. článku 119. E-ISSN 1420-3049
R&D Projects: GA ČR(CZ) GA21-15936S
Research Infrastructure: e-INFRA CZ - 90140
Institutional support: RVO:61388971
Keywords : molecular-dynamics * gromacs * poly(ethylene-terephthalate) * molecular dynamics (MD) simulations * PETase * bhet * pet * ionic liquids (ILs)
OECD category: Biochemistry and molecular biology
Impact factor: 4.6, year: 2022
Method of publishing: Open access
https://www.mdpi.com/1420-3049/27/1/119
Permanent Link: http://hdl.handle.net/11104/0331469 - 7.0547429 - MBÚ 2022 RIV CH eng J - Journal Article
Shaposhnikova, Anastasiia - Kutý, M. - Chaloupková, R. - Damborský, J. - Smatanová, I.K. - Minofar, Babak - Prudnikova, T.
Stabilization of Haloalkane Dehalogenase Structure by Interfacial Interaction with Ionic Liquids.
Crystals. Roč. 11, č. 9 (2021), č. článku 1052. ISSN 2073-4352. E-ISSN 2073-4352
R&D Projects: GA MŠMT(CZ) LM2015047
Research Infrastructure: e-INFRA CZ - 90140; RECETOX RI - 90121
Institutional support: RVO:61388971
Keywords : haloalkane dehalogenase (HLD) * ionic liquids (ILs) * molecular dynamics (MD) simulations * protein stability * 2-hydroxyethylammonium acetate ([ETA][ACC]) * 1-butyl-3-methylimidazolium methyl sulfate ([EMIM][CHS])
OECD category: Biophysics
Impact factor: 2.670, year: 2021
Method of publishing: Open access
https://www.mdpi.com/2073-4352/11/9/1052
Permanent Link: http://hdl.handle.net/11104/0323664 - 8.0540054 - 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 - 9.0524372 - MBÚ 2021 RIV CZ eng J - Journal Article
Kulik, Natalia - Kutý, Michal - Řeha, David
The study of conformational changes in photosystem II during a charge separation.
Journal of Molecular Modeling. Roč. 26, č. 4 (2020), č. článku 75. ISSN 1610-2940. E-ISSN 0948-5023
R&D Projects: GA ČR GA15-12816S
Research Infrastructure: CESNET II - 90042
Institutional support: RVO:61388971
Keywords : MD simulations * Photosystem II reaction center * Proton-coupled reduction
OECD category: Microbiology
Impact factor: 1.810, year: 2020
Method of publishing: Limited access
https://link.springer.com/article/10.1007/s00894-020-4332-9
Permanent Link: http://hdl.handle.net/11104/0308731 - 10.0523810 - ÚOCHB 2021 RIV US eng J - Journal Article
Šebesta, F. - Šebera, Jakub - Sychrovský, Vladimír - Tanaka, Y. - Burda, J. V.
QM and QM/MM umbrella sampling MD study of the formation of Hg(II)–thymine bond: Model for evaluation of the reaction energy profiles in solutions with constant pH.
Journal of Computational Chemistry. Roč. 41, č. 16 (2020), s. 1509-1520. ISSN 0192-8651. E-ISSN 1096-987X
R&D Projects: GA ČR(CZ) GA18-14990S
Institutional support: RVO:61388963
Keywords : ab initio molecular dynamics (MD) simulations * metal–NA base interactions * QM/MM calculations * thermodynamics
OECD category: Physical chemistry
Impact factor: 3.376, year: 2020
Method of publishing: Limited access
https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.26194
Permanent Link: http://hdl.handle.net/11104/0308102