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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
 

0564010 - ÚTAM 2023 RIV GB eng J - Journal Article
Hlobil, M. - Kumpová, Ivana - Hlobilová, A.
Surface area and size distribution of cement particles in hydrating paste as indicators for the conceptualization of a cement paste representative volume element.
Cement and Concrete Composites. Roč. 134, November (2022), č. článku 104798. ISSN 0958-9465. E-ISSN 1873-393X
R&D Projects: GA ČR(CZ) GJ19-25163Y
Keywords : hydration modeling * microstructure characterization * particle size distribution * Portland cement paste * specific surface area * X-ray micro-computed tomography
OECD category: Composites (including laminates, reinforced plastics, cermets, combined natural and synthetic fibre fabrics
Impact factor: 10.5, year: 2022
Method of publishing: Open access
https://doi.org/10.1016/j.cemconcomp.2022.104798
Permanent Link: https://hdl.handle.net/11104/0335770

0561647 - ÚBO 2023 RIV US eng J - Journal Article
Chen, F. - Wang, Y. - He, J. - Chen, L. - Xue, G. - Zhao, Y. - Peng, Y. - Smith, Carl - Zhang, J. - Chen, J. - Xie, P.
Molecular mechanisms of spawning habits for the adaptive radiation of endemic East Asian cyprinid fishes.
Research. Roč. 2022, SEP (2022), č. článku 9827986. ISSN 2096-5168. E-ISSN 2639-5274
Institutional support: RVO:68081766
Keywords : permeability transition pore * catalyzed cross-linking * tissue transglutaminase * fertilization envelope * ecological speciation * outer layer * hydration * adhesion * actin
OECD category: Zoology
Impact factor: 11, year: 2022
Method of publishing: Open access
https://spj.sciencemag.org/journals/research/2022/9827986/
Permanent Link: https://hdl.handle.net/11104/0334272

0559924 - ÚOCHB 2023 RIV NL eng J - Journal Article
Najgebauer, P. - Staś, M. - Wrzalik, R. - Broda, M. A. - Wieczorek, P. P. - Andrushchenko, Valery - Kupka, T.
Muscimol hydration and vibrational spectroscopy - The impact of explicit and implicit water.
Journal of Molecular Liquids. Roč. 363, October (2022), č. článku 119870. ISSN 0167-7322. E-ISSN 1873-3166
R&D Projects: GA MŠMT(CZ) EF16_019/0000729
Institutional support: RVO:61388963
Keywords : molecular dynamics (MD) * muscimol * density functional theory (DFT) * tautomers * hydrogen bonds * hydration energy
OECD category: Physical chemistry
Impact factor: 6, year: 2022
Method of publishing: Open access
https://doi.org/10.1016/j.molliq.2022.119870
Permanent Link: https://hdl.handle.net/11104/0333046

0556299 - GFÚ 2023 RIV US eng J - Journal Article
Geersen, J. - Sippl, Christian - Harmon, N.
Impact of bending-related faulting and oceanic-plate topography on slab hydration and intermediate-depth seismicity.
Geosphere. Roč. 18, č. 2 (2022), s. 562-584. ISSN 1553-040X. E-ISSN 1553-040X
Institutional support: RVO:67985530
Keywords : hydration state * oceanic plate * seismic zones
OECD category: Volcanology
Impact factor: 2.5, year: 2022
Method of publishing: Open access
https://pubs.geoscienceworld.org/gsa/geosphere/article/18/2/562/611956/Impact-of-bending-related-faulting-and-oceanic
Permanent Link: http://hdl.handle.net/11104/0330586