Dataset Open Access

Solvated protein fragments

Unke, Oliver Thorsten; Meuwly, Markus


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  <identifier identifierType="DOI">10.5281/zenodo.2605372</identifier>
  <creators>
    <creator>
      <creatorName>Unke, Oliver Thorsten</creatorName>
      <givenName>Oliver Thorsten</givenName>
      <familyName>Unke</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-7503-406X</nameIdentifier>
      <affiliation>University of Basel</affiliation>
    </creator>
    <creator>
      <creatorName>Meuwly, Markus</creatorName>
      <givenName>Markus</givenName>
      <familyName>Meuwly</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-7930-8806</nameIdentifier>
      <affiliation>University of Basel</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Solvated protein fragments</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2019</publicationYear>
  <subjects>
    <subject>proteins</subject>
    <subject>amons</subject>
    <subject>condensed phase</subject>
    <subject>quantum chemistry</subject>
    <subject>density functional theory</subject>
    <subject>DFT</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2019-03-25</date>
  </dates>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/2605372</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="arXiv" relationType="IsDocumentedBy">arXiv:1902.08408</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.2605371</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="http://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;The solvated protein fragments dataset probes many-body intermolecular interactions between&amp;nbsp;&lt;br&gt;
&amp;quot;protein fragments&amp;quot; and water molecules, which are important for the description of many&amp;nbsp;&lt;br&gt;
biologically relevant condensed phase systems. It contains structures for all possible&amp;nbsp;&lt;br&gt;
&amp;quot;amons&amp;quot; [1] (hydrogen-saturated covalently bonded fragments) of up to eight heavy atoms&amp;nbsp;&lt;br&gt;
(C, N, O, S) that can be derived from chemical graphs of proteins containing the 20 natural&lt;br&gt;
amino acids connected via peptide bonds or disulfide bridges. For amino acids that can occur&amp;nbsp;&lt;br&gt;
in different charge states due to (de-)protonation (i.e. carboxylic acids that can be&amp;nbsp;&lt;br&gt;
negatively charged or amines that can be positively charged), all possible structures with&amp;nbsp;&lt;br&gt;
up to a total charge of +-2e are included. In total, the dataset provides reference energies,&amp;nbsp;&lt;br&gt;
forces, and dipole moments for 2731180 structures calculated at the revPBE-D3(BJ)/def2-TZVP&amp;nbsp;&lt;br&gt;
level of theory [2-5] using the ORCA 4.0.1 code [6,7].&amp;nbsp;&lt;/p&gt;

&lt;p&gt;For more details, see https://arxiv.org/abs/1902.08408.&lt;/p&gt;

&lt;p&gt;[1] Huang, B. and von Lilienfeld, O. A. arXiv:1707.04146 (2017).&lt;br&gt;
[2] Grimme, S.; Antony, J.; Ehrlich, S. and Krieg, H. J. Chem. Phys. 132, 154104 (2010).&lt;br&gt;
[3] Grimme, S.; Ehrlich, S. and Goerigk, L. J. Comput. Chem. 32, 1456-1465 (2011).&lt;br&gt;
[4] Weigend, F. and Ahlrichs, R. Phys. Chem. Chem. Phys. 7, 3297-3305 (2005).&lt;br&gt;
[5] Zhang, Y. and Yang, W. Phys. Rev. Lett. 80, 890 (1998).&lt;br&gt;
[6] Neese, F. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2, 73-78 (2012).&lt;br&gt;
[7] Neese, F. Wiley Interdiscip. Rev. Comput. Mol. Sci. 8, e1327 (2018).&lt;/p&gt;</description>
  </descriptions>
</resource>
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