Dataset Open Access

Cellulose test MD dataset for analysis with Galaxy and BRIDGE

Barnett, Christopher; Naidoo, Kevin; Senapathi, Tharindu


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  <identifier identifierType="DOI">10.5281/zenodo.2537734</identifier>
  <creators>
    <creator>
      <creatorName>Barnett, Christopher</creatorName>
      <givenName>Christopher</givenName>
      <familyName>Barnett</familyName>
    </creator>
    <creator>
      <creatorName>Naidoo, Kevin</creatorName>
      <givenName>Kevin</givenName>
      <familyName>Naidoo</familyName>
    </creator>
    <creator>
      <creatorName>Senapathi, Tharindu</creatorName>
      <givenName>Tharindu</givenName>
      <familyName>Senapathi</familyName>
    </creator>
  </creators>
  <titles>
    <title>Cellulose test MD dataset for analysis with Galaxy and BRIDGE</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2019</publicationYear>
  <subjects>
    <subject>cellulase</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2019-01-11</date>
  </dates>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/2537734</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.2537733</relatedIdentifier>
  </relatedIdentifiers>
  <version>1.0.0</version>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&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;</description>
  </descriptions>
</resource>
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