Search results
- 1.0585201 - ÚMG 2025 RIV CH eng J - Journal Article
Sulimenko, Vadym - Sládková, Vladimíra - Sulimenko, Tetyana - Dráberová, Eduarda - Vosecká, Věra - Dráberová, Lubica - Skalli, O. - Dráber, Pavel
Regulation of microtubule nucleation in mouse bone marrow-derived mast cells by ARF GTPase-activating protein GIT2.
Frontiers in Immunology. Roč. 15, Feb (2024), č. článku 1321321. ISSN 1664-3224. E-ISSN 1664-3224
R&D Projects: GA MŠMT LX22NPO5102; GA ČR GA21-30281S; GA ČR(CZ) GA23-07736S; GA MŠMT LTAUSA19118; GA MŠMT(CZ) LUC23123; GA MŠMT(CZ) LM2023050
Institutional support: RVO:68378050
Keywords : gamma-tubulin * kinase-c * immune-system * complexes * identification * degranulation * receptor * src * fyn * localization * mast cells * centrosome * G protein-coupled receptor kinase-interacting protein 2 (GIT2) * microtubule nucleation * protein kinase C (PKC)
OECD category: Immunology
Impact factor: 7.3, year: 2022
Method of publishing: Open access
https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1321321/full
Permanent Link: https://hdl.handle.net/11104/0352947 - 2.0584789 - ÚFE DATA Scientific data 2024
Pandey, Saurabh K. - Cifra, Michal
Raw data of the molecular dynamics simulation trajectories and normal mode analyses of tubulin heterodimer A2205.
Description: This dataset contains data from molecular dynamics (MD) simulations and normal mode analysis (NMA) performed on tubulin protein.
MD_parameters-structure.zip: Tubulin_dimer_model.pdb containing tubulin structure, .mdp files containing parameters for MD simulation and MD.xtc file containing the trajectory of 500ns long MD simulation.
NMA_parameters-structures.zip: .mdp files containing parameter files for NMA and five structure files as an example of each type of system containing protein with different water layers as .pdb files.
NMA was performed on five types of systems, containing different water shells around protein: protein with - no water, 3Å, 5Å, 8Å, and 10Å of water. One hundred calculations were performed for each type of system above. Results obtained and analyzed in NMA calculations are provided here: frequency and eigenvectors for first one thousand eigenmodes for each NMA calculation.
frequency_files.zip: contains five folders named as frequency_0A, frequency_3A, frequency_5A, frequency_8A, and frequency_10A for systems with no water, 3Å, 5Å, 8Å, and 10Å water layer around protein. Each of these folders contain one hundred .xvg files with frequencies of normal modes.
eigenvec-files_0A.zip: one hundred .trr files containing first one thousands eigenmodes obtained from NMA for systems with only protein (i.e. no water).
eigenvec-files_3A.zip: one hundred .trr files containing first one thousands eigenmodes obtained from NMA for systems with 3Å water layer around protein.
eigenvec-files_5A|_p1.zip: fifty .trr files containing first one thousands eigenmodes obtained from NMA for systems with 5Å water layer around protein.
eigenvec-files_5A|_p2.zip: fifty .trr files containing first one thousands eigenmodes obtained from NMA for systems with 5Å water layer around protein.
eigenvec-files_8A|_p1.zip: fifty .trr files containing first one thousands eigenmodes obtained from NMA for systems with 8Å water layer around protein.
eigenvec-files_8A|_p2.zip: fifty .trr files containing first one thousands eigenmodes obtained from NMA for systems with 8Å water layer around protein.
eigenvec-files_10A|_p1.zip: fifty .trr files containing first one thousands eigenmodes obtained from NMA for systems with 10Å water layer around protein.
eigenvec-files_10A|_p2.zip: fifty .trr files containing first one thousands eigenmodes obtained from NMA for systems with 10Å water layer around protein.
Keywords : normal mode analysis * tubulin * subTHz * hydration shell
OECD category: Atomic, molecular and chemical physics (physics of atoms and molecules including collision, interaction with radiation, magnetic resonances, Mössbauer effect)
DOI: https://doi.org/10.57680/asep.0584789
Handle: https://hdl.handle.net/11104/0352684
Depositor: admin
Date of release: 4.4.2024
License: CC BY-NC-SA 4.0 - Attribution-Non-Commercial-ShareAlike-International license
File Download Size Commentary Access MD_parameters-structure.zip File list 7 44.5 GB open-access eigenvec-files_10A_p2.zip File list 4 47.2 GB open-access eigenvec-files_10A_p1.zip File list 5 43.2 GB open-access eigenvec-files_8A_p2.zip File list 5 41.6 GB open-access eigenvec-files_8A_p1.zip File list 7 38.2 GB open-access eigenvec-files_3A.zip File list 5 48.8 GB open-access eigenvec-files_0A.zip File list 5 31.2 GB open-access eigenvec-files_5A_p1.zip File list 5 27.9 GB open-access eigenvec-files_5A_p2.zip File list 5 34.1 GB open-access NMA_parameters-structures.zip File list 4 2.2 MB open-access frequency_files.zip File list 7 6.3 MB open-access R&D Projects: GA ČR(CZ) GX20-06873X; GA MŠMT(CZ) LM90254
Institutional support: RVO:67985882 - 3.0583653 - BC 2024 RIV US eng J - Journal Article
Schwark, M. - Yerena, Jose Alberto Martinez - Roehrborn, K. - Hrouzek, P. - Divoká, P. - Štenclová, Lenka - Delawská, K. - Enke, H. - Vorreiter, C. - Wiley, F. - Sippl, W. - Sobotka, R. - Saha, S. - Wilde, S. B. - Mareš, Jan - Niedermeyer, T. H. J.
More than just an eagle killer: The freshwater cyanobacterium iAetokthonos hydrillicola/i produces highly toxic dolastatin derivatives.
Proceedings of the National Academy of Sciences of the United States of America. Roč. 120, č. 40 (2023), č. článku e2219230120. ISSN 0027-8424. E-ISSN 1091-6490
R&D Projects: GA ČR(CZ) GC19-21649J
Institutional support: RVO:60077344
Keywords : antineoplastic agents * anticancer * inhibition * tubulin * cyanotoxin * cytotoxicity * aetokthonostatin * dolastatin
OECD category: Marine biology, freshwater biology, limnology
Impact factor: 11.1, year: 2022
Method of publishing: Open access
https://doi.org/10.1073/pnas.2219230120
Permanent Link: https://hdl.handle.net/11104/0351681 - 4.0582359 - MBÚ 2024 RIV US eng J - Journal Article
Schwark, M. - Martinez Yerena, Jose A. - Roehrborn, K. - Hrouzek, Pavel - Divoká, Petra - Štenclová, L. - Delawská, Kateřina - Enke, H. - Vorreiter, C. - Wiley, F. - Sippl, W. - Sobotka, Roman - Saha, Subhasish - Wilde, Susan B. - Mareš, Jan - Niedermeyer, T. H. J.
More than just an eagle killer: The freshwater cyanobacterium Aetokthonos hydrillicola produces highly toxic dolastatin derivatives.
Proceedings of the National Academy of Sciences of the United States of America. Roč. 120, č. 40 (2023), č. článku e2219230120. ISSN 0027-8424. E-ISSN 1091-6490
R&D Projects: GA ČR(CZ) GC19-21649J
Institutional support: RVO:61388971
Keywords : antineoplastic agents * marine * anticancer * analog * inhibition * tubulin * biosynthesis * efficacy * targets * binding * cyanotoxin * cytotoxicity * aetokthonostatin * dolastatin * biosynthesis
OECD category: Microbiology
Impact factor: 11.1, year: 2022
Method of publishing: Open access
https://www.pnas.org/doi/10.1073/pnas.2219230120
Permanent Link: https://hdl.handle.net/11104/0350572 - 5.0578923 - BTÚ 2024 RIV US eng M - Monography Chapter
Mikešová, Jana - Ondráková, Markéta - Jelínková, Iva - Ptáček, Jakub - Nováková, Zora - Bařinka, Cyril
Determining Potency of Inhibitors Targeting Histone Deacetylase 6 by Quantification of Acetylated Tubulin in Cells.
HDAC/HAT Function Assessment and Inhibitor Development. Vol. 2589. New York: Springer Nature, 2023, s. 455-466. ISBN 978-1-0716-2788-4
R&D Projects: GA ČR(CZ) GA21-31806S
Institutional support: RVO:86652036
Keywords : Acetyl-histone * Acetyl-tubulin * Monoclonal antibody 6-11B-1 * Quantitative Western blotting
OECD category: Biochemistry and molecular biology
https://link.springer.com/protocol/10.1007/978-1-0716-2788-4_29
Permanent Link: https://hdl.handle.net/11104/0347838 - 6.0571903 - BC 2023 RIV CH eng J - Journal Article
Tuska-Szalay, B. - Sipos, G. - Takács, N. - Kontschán, J. - Sándor, A. D. - Péter, Á. - Berta, K. - Kerek, A. - Jerzsele, A. - Votýpka, Jan - Hornok, S.
Molecular epidemiological study of Trichomonas gallinae focusing on central and southeastern Europe.
Frontiers in Veterinary Science. Roč. 9, DEC (2022), č. článku 1050561. E-ISSN 2297-1769
Institutional support: RVO:60077344
Keywords : Trichomonadea * 18S rRNA gene * alpha-tubulin gene * Columbiformes * pigeon * dove
OECD category: Veterinary science
Impact factor: 3.2, year: 2022
Method of publishing: Open access
https://www.frontiersin.org/articles/10.3389/fvets.2022.1050561/full
Permanent Link: https://hdl.handle.net/11104/0342791 - 7.0571548 - BTÚ 2024 RIV CH eng J - Journal Article
Ptáček, Jakub - Šnajdr, Ivan - Schimer, Jiří - Kutil, Zsofia - Mikesova, Jana - Baranová, Petra - Havlínová, Barbora - Tueckmantel, W. - Majer, Pavel - Kozikowski, A. - Bařinka, Cyril
Selectivity of Hydroxamate- and Difluoromethyloxadiazole-Based Inhibitors of Histone Deacetylase 6 In Vitro and in Cells.
International Journal of Molecular Sciences. Roč. 24, č. 5 (2023), č. článku 4720. E-ISSN 1422-0067
R&D Projects: GA ČR(CZ) GA21-31806S; GA MŠMT LX22NPO5102
Institutional support: RVO:86652036 ; RVO:61388963
Keywords : metallohydrolase * histone deacetylase * inhibitor profiling * tubulin * histone acetylation * nanoBRET
OECD category: Biochemistry and molecular biology
Impact factor: 5.6, year: 2022
Method of publishing: Open access
https://www.mdpi.com/1422-0067/24/5/4720
Permanent Link: https://hdl.handle.net/11104/0342903 - 8.0570259 - ÚFE 2024 RIV NL eng J - Journal Article
Průša, Jiří - Cifra, Michal
Electro-detachment of kinesin motor domain from microtubule in silico.
Computational and Structural Biotechnology Journal. Roč. 21, FEB 2023 (2023), s. 1349-1361. ISSN 2001-0370. E-ISSN 2001-0370
R&D Projects: GA ČR(CZ) GX20-06873X
Grant - others:Ministerstvo školství, mládeže a tělovýchovy - GA MŠk(CZ) LM2018140
Institutional support: RVO:67985882
Keywords : Electric field * Proteins * Tubulin * Microtubules * Molecular dynamics simulation
OECD category: Biophysics
Impact factor: 6, year: 2022
Method of publishing: Limited access
Permanent Link: https://hdl.handle.net/11104/0345167File Download Size Commentary Version Access UFE 0570259.pdf 3 7 MB Other require Scientific data in ASEP :
Raw data for the paper Molecular dynamics simulation trajectories dataset of a kinesin on tubulin heterodimers in electric field A2103 - 9.0570212 - BTÚ 2024 RIV GB eng J - Journal Article
Genova, M. - Gryčová, Lenka - Puttrich, Verena - Magiera, M. M. - Lánský, Zdeněk - Janke, C. - Braun, Marcus
Tubulin polyglutamylation differentially regulates microtubule-interacting proteins.
EMBO Journal. Roč. 42, č. 5 (2023). ISSN 0261-4189. E-ISSN 1460-2075
R&D Projects: GA ČR(CZ) GX19-27477X; GA ČR(CZ) GA22-11753S; GA MŠMT(CZ) LM2015043; GA MŠMT(CZ) LM2018129; GA MŠMT(CZ) EF16_013/0001775
Institutional support: RVO:86652036
Keywords : katanin * kinesin-1 * microtubule-associated Tau * microtubules * polyglutamylation * tubulin posttranslational modifications
OECD category: Biochemistry and molecular biology
Impact factor: 11.4, year: 2022
Method of publishing: Open access
https://www.embopress.org/doi/full/10.15252/embj.2022112101
Permanent Link: https://hdl.handle.net/11104/0342621 - 10.0568672 - ÚMG 2023 RIV CZ cze L - Prototype, f. module
Dráber, Pavel
Prototyp iPCR detekční soupravy GST.
[GST iPCR detection set.]
Internal code: TP01010060-V28 ; 2022
Technical parameters: Souprava pro detekci γ-tubulinu. Principem testu je imuno-PCR (iPCR) využívající protilátku GST. Detekční metoda, vhodná pro detekci nízkých koncentrací tubulinu v komplexních biologických vzorcích, je založená na dvojici protilátek specifických pro tubulin, z nichž jedna je značená biotinem. Využívá iPCR amplifikační systém, kde biotinylovaná protilátka je detegována pomocí extravidinu a biotinylovaných DNA molekul
Economic parameters: Přínos vyšší desítky až nižší statisíce Kč ročně využitím vlastníkem
R&D Projects: GA TA ČR TP01010060
Institutional support: RVO:68378050
Keywords : iPCR * tubulin * detection
OECD category: Biochemistry and molecular biology
Permanent Link: https://hdl.handle.net/11104/0339940