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
R&D Projects: GA ČR(CZ) GX20-06873X; GA MŠMT(CZ) LM90254
Institutional support: RVO:67985882
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