Dataset Open Access

Cellulose test MD dataset for analysis with Galaxy and BRIDGE

Barnett, Christopher; Naidoo, Kevin; Senapathi, Tharindu


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{
  "publisher": "Zenodo", 
  "DOI": "10.5281/zenodo.2537734", 
  "title": "Cellulose test MD dataset for analysis with Galaxy and BRIDGE", 
  "issued": {
    "date-parts": [
      [
        2019, 
        1, 
        11
      ]
    ]
  }, 
  "abstract": "<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>", 
  "author": [
    {
      "family": "Barnett, Christopher"
    }, 
    {
      "family": "Naidoo, Kevin"
    }, 
    {
      "family": "Senapathi, Tharindu"
    }
  ], 
  "version": "1.0.0", 
  "type": "dataset", 
  "id": "2537734"
}
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