Research Data Leeds Repository

Study of the flexibility of GroEL through FFEA simulation and analysis

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/10.5518/209¹

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 science2 F000 - Physical sciences > F300 - Physics > F340 - Mathematical & theoretical physics > F343 - Computational physics3
Divisions:	Faculty of Engineering and Physical Sciences > School of Physics and Astronomy4
Related resources:	Location Type https://doi.org/10.1371/journal.pcbi.10058975 Publication https://eprints.whiterose.ac.uk/125482/6 Publication https://doi.org/10.5518/3187 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/1638
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/0000-0003-4857-02409 University of Leeds https://ror.org/024mrxd33 ror Hanson, Benjamin S. https://orcid.org/0000-0002-6079-450610 University of Leeds https://ror.org/024mrxd33 ror Richardson, Robin A. https://orcid.org/0000-0002-9984-272011 University College London https://ror.org/02jx3x895 ror Welch, Robert https://orcid.org/0000-0002-0135-011212 University of Leeds https://ror.org/024mrxd33 ror Harris, Sarah A. https://orcid.org/0000-0002-2812-165113 University of Leeds https://ror.org/024mrxd33 ror Read, Daniel J. https://orcid.org/0000-0003-1194-927314 University of Leeds https://ror.org/024mrxd33 ror Harlen, Oliver G. https://orcid.org/0000-0002-4593-354715 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.uk16 Last Modified: 15 Aug 2024 12:31

Files

Documentation

readme.txt [845B] 17 readme.txt [845B] 18 readme.txt [845B] 19 Security: Anyone File name: readme.txt20 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] 21 emd_5043_albert_E333MPa.ffea [1kB] 22 emd_5043_albert_E333MPa.ffea [1kB] 23 Security: Anyone File name: emd_5043_albert_E333MPa.ffea24 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] 25 emd_5043_albert_E1GPa.ffea [1kB] 26 emd_5043_albert_E1GPa.ffea [1kB] 27 Security: Anyone File name: emd_5043_albert_E1GPa.ffea28 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] 29 emd_5043_albert_E333MPa_out.fcp [310B] 30 emd_5043_albert_E333MPa_out.fcp [310B] 31 Security: Anyone File name: emd_5043_albert_E333MPa_out.fcp32 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] 33 emd_5043_albert_E1GPa_out.fcp [310B] 34 emd_5043_albert_E1GPa_out.fcp [310B] 35 Security: Anyone File name: emd_5043_albert_E1GPa_out.fcp36 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] 37 emd_5043_albert.vol [398kB] 38 emd_5043_albert.vol [398kB] 39 Security: Anyone File name: emd_5043_albert.vol40 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] 41 emd_5043_albert.node [102kB] 42 emd_5043_albert.node [102kB] 43 Security: Anyone File name: emd_5043_albert.node44 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] 45 emd_5043_albert_origin.node [102kB] 46 emd_5043_albert_origin.node [102kB] 47 Security: Anyone File name: emd_5043_albert_origin.node48 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] 49 emd_5043_albert.top [62kB] 50 emd_5043_albert.top [62kB] 51 Security: Anyone File name: emd_5043_albert.top52 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] 53 emd_5043_albert.surf [90kB] 54 emd_5043_albert.surf [90kB] 55 Security: Anyone File name: emd_5043_albert.surf56 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] 57 emd_5043_albert.pin [56B] 58 emd_5043_albert.pin [56B] 59 Security: Anyone File name: emd_5043_albert.pin60 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] 61 emd_5043_albert.stokes [21kB] 62 emd_5043_albert.stokes [21kB] 63 Security: Anyone File name: emd_5043_albert.stokes64 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] 65 emd_5043_albert.vdw [14kB] 66 emd_5043_albert.vdw [14kB] 67 Security: Anyone File name: emd_5043_albert.vdw68 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] 69 emd_5043_albert.lj [1kB] 70 emd_5043_albert.lj [1kB] 71 Security: Anyone File name: emd_5043_albert.lj72 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] 73 emd_5043_albert.mat [75kB] 74 emd_5043_albert.mat [75kB] 75 Security: Anyone File name: emd_5043_albert.mat76 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] 77 emd_5043_albert_E333MPa.mat [74kB] 78 emd_5043_albert_E333MPa.mat [74kB] 79 Security: Anyone File name: emd_5043_albert_E333MPa.mat80 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] 81 emd_5043_albert_E1GPa.mat [75kB] 82 emd_5043_albert_E1GPa.mat [75kB] 83 Security: Anyone File name: emd_5043_albert_E1GPa.mat84 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] 85 emd_5043_albertto4hel.map [3MB] 86 emd_5043_albertto4hel.map [3MB] 87 Security: Anyone File name: emd_5043_albertto4hel.map88 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] 89 emd_5043_albert_E333MPa_measurement.fm [258kB] 90 emd_5043_albert_E333MPa_measurement.fm [258kB] 91 Security: Anyone File name: emd_5043_albert_E333MPa_measurement.fm92 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] 93 emd_5043_albert_E1GPa_measurement.fm [258kB] 94 emd_5043_albert_E1GPa_measurement.fm [258kB] 95 Security: Anyone File name: emd_5043_albert_E1GPa_measurement.fm96 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] 97 emd_5043_albert_E333MPa_trajectory.ftj [1GB] 98 emd_5043_albert_E333MPa_trajectory.ftj [1GB] 99 Security: Anyone File name: emd_5043_albert_E333MPa_trajectory.ftj100 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] 101 emd_5043_albert_E1GPa_trajectory.ftj [1GB] 102 emd_5043_albert_E1GPa_trajectory.ftj [1GB] 103 Security: Anyone File name: emd_5043_albert_E1GPa_trajectory.ftj104 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] 105 emd_5043_albert_E333MPa_1000frames_fitted.pdb [4GB] 106 emd_5043_albert_E333MPa_1000frames_fitted.pdb [4GB] 107 Security: Anyone File name: emd_5043_albert_E333MPa_1000frames_fitted.pdb108 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] 109 emd_5043_albert_E1GPa_1000frames_fitted.pdb [4GB] 110 emd_5043_albert_E1GPa_1000frames_fitted.pdb [4GB] 111 Security: Anyone File name: emd_5043_albert_E1GPa_1000frames_fitted.pdb112 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] 113 emd_5043_albert_E333MPa_pseudo.pcz [839kB] 114 emd_5043_albert_E333MPa_pseudo.pcz [839kB] 115 Security: Anyone File name: emd_5043_albert_E333MPa_pseudo.pcz116 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] 117 emd_5043_albert_E1GPa_pseudo.pcz [839kB] 118 emd_5043_albert_E1GPa_pseudo.pcz [839kB] 119 Security: Anyone File name: emd_5043_albert_E1GPa_pseudo.pcz120 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] 121 GroEL_3000ns_energyconv.png [120kB] 122 GroEL_3000ns_energyconv.png [120kB] 123 Security: Anyone File name: GroEL_3000ns_energyconv.png124 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] 125 GroEL_3000ns_RMSDcompare.png [125kB] 126 GroEL_3000ns_RMSDcompare.png [125kB] 127 Security: Anyone File name: GroEL_3000ns_RMSDcompare.png128 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] 129 GroEL_3000ns_PCAeigvals.png [68kB] 130 GroEL_3000ns_PCAeigvals.png [68kB] 131 Security: Anyone File name: GroEL_3000ns_PCAeigvals.png132 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] 133 GroEL_3000ns_RMSDtraces.png [115kB] 134 GroEL_3000ns_RMSDtraces.png [115kB] 135 Security: Anyone File name: GroEL_3000ns_RMSDtraces.png136 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

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• 126. https://archive.researchdata.leeds.ac.uk/163/27/GroEL_3000ns_RMSDcompare.png
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• 129. https://archive.researchdata.leeds.ac.uk/163/28/GroEL_3000ns_PCAeigvals.png
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• 133. https://archive.researchdata.leeds.ac.uk/163/29/GroEL_3000ns_RMSDtraces.png
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