Dataset Open Access

Cellulose test MD dataset for analysis with Galaxy and BRIDGE

Barnett, Christopher; Naidoo, Kevin; Senapathi, Tharindu


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{
  "description": "<p>This coordinate and trajectory dataset is that of&nbsp;cellulase and&nbsp;octaose&nbsp;substrate&nbsp;in water. It&nbsp;has been derived from the <a href=\"https://www.rcsb.org/structure/7cel\">7CEL PDB</a> structure of a fungal cellobiohydrolase.&nbsp;</p>\n\n<p>The original enzyme has been modified to revert the mutation at position&nbsp;217 and to include disulfide bonds. The octaose substrate&nbsp;is an oligosaccharide consisting&nbsp;of 8 beta 1-4 linked glucose monomers.&nbsp;&nbsp;The enzyme and substrate have been placed in a cubic TIP3P water box containing 0.15 M ions (NaCl).</p>\n\n<p>The files includes are:&nbsp;</p>\n\n<ul>\n\t<li><strong>cbh1test.pdb</strong>: the coordinates of the entire system (water, protein and substrate) in PDB format.&nbsp;</li>\n\t<li><strong>cbh1test.dcd</strong>: a short MD trajectory (16 frames) in CHARMM DCD format.</li>\n</ul>", 
  "license": "https://creativecommons.org/licenses/by/4.0/legalcode", 
  "creator": [
    {
      "@type": "Person", 
      "name": "Barnett, Christopher"
    }, 
    {
      "@type": "Person", 
      "name": "Naidoo, Kevin"
    }, 
    {
      "@type": "Person", 
      "name": "Senapathi, Tharindu"
    }
  ], 
  "url": "https://zenodo.org/record/2537734", 
  "datePublished": "2019-01-11", 
  "version": "1.0.0", 
  "keywords": [
    "cellulase"
  ], 
  "@context": "https://schema.org/", 
  "distribution": [
    {
      "contentUrl": "https://zenodo.org/api/files/0e28549d-316f-4cca-9352-675f7b8f451d/cbh1test.dcd", 
      "encodingFormat": "dcd", 
      "@type": "DataDownload"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/0e28549d-316f-4cca-9352-675f7b8f451d/cbh1test.pdb", 
      "encodingFormat": "pdb", 
      "@type": "DataDownload"
    }
  ], 
  "identifier": "https://doi.org/10.5281/zenodo.2537734", 
  "@id": "https://doi.org/10.5281/zenodo.2537734", 
  "@type": "Dataset", 
  "name": "Cellulose test MD dataset for analysis with Galaxy and BRIDGE"
}
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