Dataset Open Access

Project files provided as supporting information to the manuscript "An information theory-based approach for optimal model reduction of biomolecules"

Marco Giulini; Roberto Menichetti; Raffaello Potestio


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{
  "description": "<p>The dataset contains the following files:</p>\n\n<ul>\n\t<li>- adenylate.zip</li>\n\t<li>- antitrypsin.zip</li>\n\t<li>- tamapin.zip</li>\n\t<li>- analysis_notebooks.zip</li>\n</ul>\n\n<p>Each of these refers to one of three proteins. For each CG sites number N, each compressed folder contains the following files:</p>\n\n<ul>\n\t<li>random mappings (random_mappings_${N}.txt)&nbsp;</li>\n\t<li>random mapping entropies (random_smaps_${N}.txt) [fig1]</li>\n\t<li>optimal mappings (lowest_mappings_${N}.txt) [fig3, fig4, figS2]</li>\n\t<li>optimal mapping entropies (lowest_smaps_${N}.txt) [fig1]</li>\n\t<li>pdb files with conservations probabilities in the beta factor column (${N}_probs.pdb) [fig4, figs2]</li>\n\t<li>SASA values (${protein_name}_SASA_residues.xvg&nbsp;</li>\n\t<li>transition mapping entropies (${protein_name}_transition_smaps.txt) [fig2]</li>\n\t<li>additional transition mapping entropies (${protein_name}_transition_smaps*) [figs3]</li>\n</ul>\n\n<p>The file&nbsp;analysis_notebooks.zip contains the python3 notebooks employed to perform all the analysis present in the paper:</p>\n\n<ul>\n\t<li>paper_analysis_adenylate.ipynb</li>\n\t<li>paper_analysis_antitrypsin.ipynb</li>\n\t<li>paper_analysis_tamapin.ipynb</li>\n</ul>\n\n<p>Packages required for the usage of these python 3 scripts:</p>\n\n<p>- numpy<br>\n- pandas<br>\n- matplotlib<br>\n- seaborn<br>\n&nbsp;</p>", 
  "license": "https://creativecommons.org/licenses/by/4.0/legalcode", 
  "creator": [
    {
      "affiliation": "University of Trento", 
      "@id": "https://orcid.org/0000-0002-2691-712X", 
      "@type": "Person", 
      "name": "Marco Giulini"
    }, 
    {
      "affiliation": "University of Trento", 
      "@id": "https://orcid.org/0000-0002-5961-6438", 
      "@type": "Person", 
      "name": "Roberto Menichetti"
    }, 
    {
      "affiliation": "University of Trento", 
      "@id": "https://orcid.org/0000-0001-6408-9380", 
      "@type": "Person", 
      "name": "Raffaello Potestio"
    }
  ], 
  "url": "https://zenodo.org/record/3776293", 
  "datePublished": "2020-04-29", 
  "@context": "https://schema.org/", 
  "distribution": [
    {
      "contentUrl": "https://zenodo.org/api/files/457c5383-343d-4411-b6f8-68b089b97011/adenylate.zip", 
      "encodingFormat": "zip", 
      "@type": "DataDownload"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/457c5383-343d-4411-b6f8-68b089b97011/analysis_notebooks.zip", 
      "encodingFormat": "zip", 
      "@type": "DataDownload"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/457c5383-343d-4411-b6f8-68b089b97011/antitrypsin.zip", 
      "encodingFormat": "zip", 
      "@type": "DataDownload"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/457c5383-343d-4411-b6f8-68b089b97011/tamapin.zip", 
      "encodingFormat": "zip", 
      "@type": "DataDownload"
    }
  ], 
  "identifier": "https://doi.org/10.5281/zenodo.3776293", 
  "@id": "https://doi.org/10.5281/zenodo.3776293", 
  "@type": "Dataset", 
  "name": "Project files provided as supporting information to the manuscript \"An information theory-based approach for optimal model reduction of biomolecules\""
}
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