Research Data Leeds Repository

Citation

Solernou, Albert and Hanson, Benjamin S. and Richardson, Robin A. and Welch, Robert and Read, Daniel J. and Harlen, Oliver G. and Harris, Sarah A. (2018) Analysis and comparison of FFEA with all-atom molecular dynamics. University of Leeds. [Dataset] https://doi.org/10.5518/318

Dataset description

Input scripts, structural information and output trajectories, measurement and analysis data of Arfaptin and xylanase, using FFEA and all-atom molecular dynamics, in order to support 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/10.5518/209 Dataset https://doi.org/10.1371/journal.pcbi.1005897 Publication https://eprints.whiterose.ac.uk/125482/ Publication
License:	Creative Commons Attribution 4.0 International (CC BY 4.0)
Date deposited:	21 Feb 2018 08:40
URI:	https://archive.researchdata.leeds.ac.uk/id/eprint/316
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 of Leeds https://ror.org/024mrxd33 ror Welch, Robert https://orcid.org/0000-0002-0135-0112 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 Harris, Sarah A. https://orcid.org/0000-0002-2812-1651 University of Leeds https://ror.org/024mrxd33 ror Type of data: Dataset Research funders: EPSRC Grant numbers: EP/M004228/1 Publication date: 2018 Resource language: English Metadata language: English Publisher: University of Leeds Contact email: a.solernou@leeds.ac.uk Last Modified: 08 Aug 2024 14:47

Files

Documentation

Readme [1kB] Readme [1kB] Readme [1kB] 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: 1kB

Data

Backbone trajectories [158MB] Backbone trajectories [158MB] Backbone trajectories [158MB] Security: Anyone File name: backbone_trajectories.zip Content type: Data Description: FFEA trajectory (.ftj) and mapped PDB format trajectories for FFEA simulations of 1TUX, 1ZVZ and 1i49, including the map itself, other FFEA files, source files for the 3D model, log files etc. Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 158MB

Backbone PCA [13MB] Backbone PCA [13MB] Backbone PCA [13MB] Security: Anyone File name: backbones_pca.zip Content type: Data Description: Principal component analysis for the backbone trajectories, generated with PyPCAZip Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 13MB

Heavy PCA [36MB] Heavy PCA [36MB] Heavy PCA [36MB] Security: Anyone File name: heavy_pca.zip Content type: Data Description: Principal component analysis for the heavy trajectories, generated with PyPCAZip Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 36MB

Heavy trajectories [765MB] Heavy trajectories [765MB] Heavy trajectories [765MB] Security: Anyone File name: heavy_trajectories.zip Content type: Data Description: FFEA trajectory (.ftj) and mapped PDB format trajectories for FFEA simulations of 1TUX, 1ZVZ and 1i49, including the map itself, other FFEA files, source files for the 3D model, log files etc. Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 765MB

Movies [45MB] Movies [45MB] Movies [45MB] Security: Anyone File name: movies.zip Content type: Data Description: Videos of each FFEA trajectory encoded in h264. Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 45MB

PCA animations [21MB] PCA animations [21MB] PCA animations [21MB] Security: Anyone File name: pca_anims.zip Content type: Data Description: Animations made from the first five components of the PCA for each molecule. Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 21MB

Self comparison PCA [12MB] Self comparison PCA [12MB] Self comparison PCA [12MB] Security: Anyone File name: self_comparison_pca.zip Content type: Data Description: Principal component analysis for two halves of the same trajectory, generated from the MoDEL trajectories for each molecule Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 12MB