Dataset Open Access

Cellulose test MD dataset for analysis with Galaxy and BRIDGE

Barnett, Christopher; Naidoo, Kevin; Senapathi, Tharindu


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    <dct:title>Cellulose test MD dataset for analysis with Galaxy and BRIDGE</dct:title>
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    <dcat:keyword>cellulase</dcat:keyword>
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    <dct:description>&lt;p&gt;This coordinate and trajectory dataset is that of&amp;nbsp;cellulase and&amp;nbsp;octaose&amp;nbsp;substrate&amp;nbsp;in water. It&amp;nbsp;has been derived from the &lt;a href="https://www.rcsb.org/structure/7cel"&gt;7CEL PDB&lt;/a&gt; structure of a fungal cellobiohydrolase.&amp;nbsp;&lt;/p&gt; &lt;p&gt;The original enzyme has been modified to revert the mutation at position&amp;nbsp;217 and to include disulfide bonds. The octaose substrate&amp;nbsp;is an oligosaccharide consisting&amp;nbsp;of 8 beta 1-4 linked glucose monomers.&amp;nbsp;&amp;nbsp;The enzyme and substrate have been placed in a cubic TIP3P water box containing 0.15 M ions (NaCl).&lt;/p&gt; &lt;p&gt;The files includes are:&amp;nbsp;&lt;/p&gt; &lt;ul&gt; &lt;li&gt;&lt;strong&gt;cbh1test.pdb&lt;/strong&gt;: the coordinates of the entire system (water, protein and substrate) in PDB format.&amp;nbsp;&lt;/li&gt; &lt;li&gt;&lt;strong&gt;cbh1test.dcd&lt;/strong&gt;: a short MD trajectory (16 frames) in CHARMM DCD format.&lt;/li&gt; &lt;/ul&gt;</dct:description>
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