Research Data Leeds Repository

Citation

Solernou, Albert and Hanson, Benjamin S. and Richardson, Robin A. and Welch, Robert and Harris, Sarah A. and Read, Daniel J. and Harlen, Oliver G. (2017) Study of the flexibility of GroEL through FFEA simulation and analysis. University of Leeds. [Dataset] https://doi.org/10.5518/209

Dataset description

Input scripts, structural information and output trajectory, measurement and analysis data of GroEL using FFEA supporting the results presented in the article "Fluctuating Finite Element Analysis (FFEA): A Continuum Mechanics Software Tool for Mesoscale Simulation of Biomolecules" in PLoS Computational Biology

Subjects:	C000 - Biological sciences > C700 - Molecular biology, biophysics & biochemistry > C770 - Biophysical science F000 - Physical sciences > F300 - Physics > F340 - Mathematical & theoretical physics > F343 - Computational physics
Divisions:	Faculty of Engineering and Physical Sciences > School of Physics and Astronomy
Related resources:	Location Type https://doi.org/10.1371/journal.pcbi.1005897 Publication https://eprints.whiterose.ac.uk/125482/ Publication https://doi.org/10.5518/318 Dataset
License:	Creative Commons Attribution 4.0 International (CC BY 4.0)
Date deposited:	29 Jun 2017 10:50
URI:	https://archive.researchdata.leeds.ac.uk/id/eprint/163
Additional details Additional details Creators or authors: Creators ORCID Other ID Email Primary affiliation Primary affiliation ID Primary affiliation ID type Secondary affiliation Secondary affiliation ID Secondary affiliation ID type Solernou, Albert https://orcid.org/0000-0003-4857-0240 University of Leeds https://ror.org/024mrxd33 ror Hanson, Benjamin S. https://orcid.org/0000-0002-6079-4506 University of Leeds https://ror.org/024mrxd33 ror Richardson, Robin A. https://orcid.org/0000-0002-9984-2720 University College London https://ror.org/02jx3x895 ror Welch, Robert https://orcid.org/0000-0002-0135-0112 University of Leeds https://ror.org/024mrxd33 ror Harris, Sarah A. https://orcid.org/0000-0002-2812-1651 University of Leeds https://ror.org/024mrxd33 ror Read, Daniel J. https://orcid.org/0000-0003-1194-9273 University of Leeds https://ror.org/024mrxd33 ror Harlen, Oliver G. https://orcid.org/0000-0002-4593-3547 University of Leeds https://ror.org/024mrxd33 ror Type of data: Dataset Research funders: EPSRC Grant numbers: EP/M004228/1 Publication date: 2017 Resource language: English Metadata language: English Publisher: University of Leeds Contact email: a.solernou@leeds.ac.uk Last Modified: 15 Aug 2024 12:31

Files

Documentation

readme.txt [845B] readme.txt [845B] readme.txt [845B] Security: Anyone File name: readme.txt Content type: Documentation Mime-Type: text/plain License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 845B

Data

emd_5043_albert_E333MPa.ffea [1kB] emd_5043_albert_E333MPa.ffea [1kB] emd_5043_albert_E333MPa.ffea [1kB] Security: Anyone File name: emd_5043_albert_E333MPa.ffea Content type: Data Description: Input file for the E = 333MPa simulation of GroEL License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 1kB

emd_5043_albert_E1GPa.ffea [1kB] emd_5043_albert_E1GPa.ffea [1kB] emd_5043_albert_E1GPa.ffea [1kB] Security: Anyone File name: emd_5043_albert_E1GPa.ffea Content type: Data Description: Input file for the E = 1GPa simulation of GroEL License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 1kB

emd_5043_albert_E333MPa_out.fcp [310B] emd_5043_albert_E333MPa_out.fcp [310B] emd_5043_albert_E333MPa_out.fcp [310B] Security: Anyone File name: emd_5043_albert_E333MPa_out.fcp Content type: Data Description: Checkpoint file to restart the E = 333MPa simulation of GroEL License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 310B

emd_5043_albert_E1GPa_out.fcp [310B] emd_5043_albert_E1GPa_out.fcp [310B] emd_5043_albert_E1GPa_out.fcp [310B] Security: Anyone File name: emd_5043_albert_E1GPa_out.fcp Content type: Data Description: Checkpoint file to restart the E = 1GPa simulation of GroEL License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 310B

emd_5043_albert.vol [398kB] emd_5043_albert.vol [398kB] emd_5043_albert.vol [398kB] Security: Anyone File name: emd_5043_albert.vol Content type: Data Description: Volumetric Data generated from the FFEA initialisation procedure for the GroEL structure License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 398kB

emd_5043_albert.node [102kB] emd_5043_albert.node [102kB] emd_5043_albert.node [102kB] Security: Anyone File name: emd_5043_albert.node Content type: Data Description: Node file (initial position data) for an FFEA simulation of GroEL License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 102kB

emd_5043_albert_origin.node [102kB] emd_5043_albert_origin.node [102kB] emd_5043_albert_origin.node [102kB] Security: Anyone File name: emd_5043_albert_origin.node Content type: Data Description: Node file (initial position data) with centroid translated to the origin for an FFEA simulation of GroEL License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 102kB

emd_5043_albert.top [62kB] emd_5043_albert.top [62kB] emd_5043_albert.top [62kB] Security: Anyone File name: emd_5043_albert.top Content type: Data Description: Topology file (3D node connectivity data) for an FFEA simulation of GroEL License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 62kB

emd_5043_albert.surf [90kB] emd_5043_albert.surf [90kB] emd_5043_albert.surf [90kB] Security: Anyone File name: emd_5043_albert.surf Content type: Data Description: Surface file (surface node connectivity data) for an FFEA simulation of GroEL License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 90kB

emd_5043_albert.pin [56B] emd_5043_albert.pin [56B] emd_5043_albert.pin [56B] Security: Anyone File name: emd_5043_albert.pin Content type: Data Description: Pin file (list of node indices that are motionless) for an FFEA simulation of GroEL License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 56B

emd_5043_albert.stokes [21kB] emd_5043_albert.stokes [21kB] emd_5043_albert.stokes [21kB] Security: Anyone File name: emd_5043_albert.stokes Content type: Data Description: Stokes file (local hydrodynamic radius data) for an FFEA simulation of GroEL License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 21kB

emd_5043_albert.vdw [14kB] emd_5043_albert.vdw [14kB] emd_5043_albert.vdw [14kB] Security: Anyone File name: emd_5043_albert.vdw Content type: Data Description: VdW file (list of integers specifying the Van der Waals interaction type) for an FFEA simulation of GroEL License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 14kB

emd_5043_albert.lj [1kB] emd_5043_albert.lj [1kB] emd_5043_albert.lj [1kB] Security: Anyone File name: emd_5043_albert.lj Content type: Data Description: LJ file (parameter pair matrix defining VdW interactions and strengths) for an FFEA simulation of GroEL License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 1kB

emd_5043_albert.mat [75kB] emd_5043_albert.mat [75kB] emd_5043_albert.mat [75kB] Security: Anyone File name: emd_5043_albert.mat Content type: Data Description: Material file (structural parameter data) for an FFEA simulation of GroEL (Default) License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 75kB

emd_5043_albert_E333MPa.mat [74kB] emd_5043_albert_E333MPa.mat [74kB] emd_5043_albert_E333MPa.mat [74kB] Security: Anyone File name: emd_5043_albert_E333MPa.mat Content type: Data Description: Material file (structural parameter data) for an FFEA simulation of GroEL (Youngs Modulus, E = 333MPa) License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 74kB

emd_5043_albert_E1GPa.mat [75kB] emd_5043_albert_E1GPa.mat [75kB] emd_5043_albert_E1GPa.mat [75kB] Security: Anyone File name: emd_5043_albert_E1GPa.mat Content type: Data Description: Material file (structural parameter data) for an FFEA simulation of GroEL (Youngs Modulus, E = 1GPa) License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 75kB

emd_5043_albertto4hel.map [3MB] emd_5043_albertto4hel.map [3MB] emd_5043_albertto4hel.map [3MB] Security: Anyone File name: emd_5043_albertto4hel.map Content type: Data Description: Map file containing a sparse matrix (Yale format) which, when applied to the FFEA trajectory frame, produces a pseudo-atomic GroEL frame using PDB ID:4HEL License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 3MB

emd_5043_albert_E333MPa_measurement.fm [258kB] emd_5043_albert_E333MPa_measurement.fm [258kB] emd_5043_albert_E333MPa_measurement.fm [258kB] Security: Anyone File name: emd_5043_albert_E333MPa_measurement.fm Content type: Data Description: Measurement file, containing strain, kinetic and electrostatic energies, RMSD, centroid position etc, resulting from E = 333MPa FFEA simulation of GroEL Mime-Type: application/vnd.framemaker License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 258kB

emd_5043_albert_E1GPa_measurement.fm [258kB] emd_5043_albert_E1GPa_measurement.fm [258kB] emd_5043_albert_E1GPa_measurement.fm [258kB] Security: Anyone File name: emd_5043_albert_E1GPa_measurement.fm Content type: Data Description: Measurement file, containing strain, kinetic and electrostatic energies, RMSD, centroid position etc, resulting from E = 1GPa FFEA simulation of GroEL Mime-Type: application/vnd.framemaker License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 258kB

emd_5043_albert_E333MPa_trajectory.ftj [1GB] emd_5043_albert_E333MPa_trajectory.ftj [1GB] emd_5043_albert_E333MPa_trajectory.ftj [1GB] Security: Anyone File name: emd_5043_albert_E333MPa_trajectory.ftj Content type: Data Description: Trajectory file, containing all node positions for every nth simulation frame, resulting from E = 333MPa FFEA simulation of GroEL License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 1GB

emd_5043_albert_E1GPa_trajectory.ftj [1GB] emd_5043_albert_E1GPa_trajectory.ftj [1GB] emd_5043_albert_E1GPa_trajectory.ftj [1GB] Security: Anyone File name: emd_5043_albert_E1GPa_trajectory.ftj Content type: Data Description: Trajectory file, containing all node positions for every nth simulation frame, resulting from E = 1GPa FFEA simulation of GroEL License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 1GB

emd_5043_albert_E333MPa_1000frames_fitted.pdb [4GB] emd_5043_albert_E333MPa_1000frames_fitted.pdb [4GB] emd_5043_albert_E333MPa_1000frames_fitted.pdb [4GB] Security: Anyone File name: emd_5043_albert_E333MPa_1000frames_fitted.pdb Content type: Data Description: PDB file, containing a 1000 frame pseudo-atomic trajectory mapped from the E = 333MPa FFEA simulation of GroEL, and aligned with the average structure Mime-Type: application/vnd.palm License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 4GB

emd_5043_albert_E1GPa_1000frames_fitted.pdb [4GB] emd_5043_albert_E1GPa_1000frames_fitted.pdb [4GB] emd_5043_albert_E1GPa_1000frames_fitted.pdb [4GB] Security: Anyone File name: emd_5043_albert_E1GPa_1000frames_fitted.pdb Content type: Data Description: PDB file, containing a 1000 frame pseudo-atomic trajectory mapped from the E = 1GPa FFEA simulation of GroEL, and aligned with the average structure Mime-Type: application/vnd.palm License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 4GB

emd_5043_albert_E333MPa_pseudo.pcz [839kB] emd_5043_albert_E333MPa_pseudo.pcz [839kB] emd_5043_albert_E333MPa_pseudo.pcz [839kB] Security: Anyone File name: emd_5043_albert_E333MPa_pseudo.pcz Content type: Data Description: PCZ file, containing the FFEA trajectory from the E = 333MPa FFEA simulation of GroEL compressed using principal component analysis, in the pyPcazip format License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 839kB

emd_5043_albert_E1GPa_pseudo.pcz [839kB] emd_5043_albert_E1GPa_pseudo.pcz [839kB] emd_5043_albert_E1GPa_pseudo.pcz [839kB] Security: Anyone File name: emd_5043_albert_E1GPa_pseudo.pcz Content type: Data Description: PCZ file, containing the FFEA trajectory from the E = 1GPa FFEA simulation of GroEL compressed using principal component analysis, in the pyPcazip format License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 839kB

GroEL_3000ns_energyconv.png [120kB] GroEL_3000ns_energyconv.png [120kB] GroEL_3000ns_energyconv.png [120kB] Security: Anyone File name: GroEL_3000ns_energyconv.png Content type: Data Description: Graph of the convergence of strain energy for the two FFEA simulations of GroEL Mime-Type: image/png License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 120kB

GroEL_3000ns_RMSDcompare.png [125kB] GroEL_3000ns_RMSDcompare.png [125kB] GroEL_3000ns_RMSDcompare.png [125kB] Security: Anyone File name: GroEL_3000ns_RMSDcompare.png Content type: Data Description: Graph comparing the non-aligned RMSD traces of the FFEA trajectory and mapped pseudo-atomic trajectory of the E = 1GPa FFEA simulation of GroEL Mime-Type: image/png License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 125kB

GroEL_3000ns_PCAeigvals.png [68kB] GroEL_3000ns_PCAeigvals.png [68kB] GroEL_3000ns_PCAeigvals.png [68kB] Security: Anyone File name: GroEL_3000ns_PCAeigvals.png Content type: Data Description: Graph comparing the spectrum of eigenvalues resulting from PCA analysis of the two FFEA simulations of GroEL Mime-Type: image/png License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 68kB

GroEL_3000ns_RMSDtraces.png [115kB] GroEL_3000ns_RMSDtraces.png [115kB] GroEL_3000ns_RMSDtraces.png [115kB] Security: Anyone File name: GroEL_3000ns_RMSDtraces.png Content type: Data Description: Graph comparing the RMSD traces following alignment with the average structure of the two FFEA simulations of GroEL Mime-Type: image/png License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 115kB