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KLIFS: A Knowledge-Based Structural Database To Navigate Kinase–Ligand Interaction Space

van Linden, Oscar P. J.; Kooistra, Albert J.; Leurs, Rob; de Esch, Iwan J. P.; de Graaf, Chris


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  <identifier identifierType="DOI">10.5281/zenodo.45414</identifier>
  <creators>
    <creator>
      <creatorName>van Linden, Oscar P. J.</creatorName>
      <givenName>Oscar P. J.</givenName>
      <familyName>van Linden</familyName>
      <affiliation>Vrije Universiteit Amsterdam</affiliation>
    </creator>
    <creator>
      <creatorName>Kooistra, Albert J.</creatorName>
      <givenName>Albert J.</givenName>
      <familyName>Kooistra</familyName>
      <affiliation>Vrije Universiteit Amsterdam</affiliation>
    </creator>
    <creator>
      <creatorName>Leurs, Rob</creatorName>
      <givenName>Rob</givenName>
      <familyName>Leurs</familyName>
      <affiliation>Vrije Universiteit Amsterdam</affiliation>
    </creator>
    <creator>
      <creatorName>de Esch, Iwan J. P.</creatorName>
      <givenName>Iwan J. P.</givenName>
      <familyName>de Esch</familyName>
      <affiliation>Vrije Universiteit Amsterdam</affiliation>
    </creator>
    <creator>
      <creatorName>de Graaf, Chris</creatorName>
      <givenName>Chris</givenName>
      <familyName>de Graaf</familyName>
      <affiliation>Vrije Universiteit Amsterdam</affiliation>
    </creator>
  </creators>
  <titles>
    <title>KLIFS: A Knowledge-Based Structural Database To Navigate Kinase–Ligand Interaction Space</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2013</publicationYear>
  <subjects>
    <subject>kinases</subject>
    <subject>Crystal structures</subject>
    <subject>Kinase-ligand interactions</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2013-08-13</date>
  </dates>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/45414</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsPartOf">10.1021/jm400378w</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsPreviousVersionOf">10.1093/nar/gkv1082</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPreviousVersionOf">http://klifs.vu-compmedchem.nl</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="http://creativecommons.org/publicdomain/zero/1.0/legalcode">Creative Commons Zero v1.0 Universal</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;The Kinase-Ligand Interaction Fingerprints and Structure database (KLIFS) contains a consistent structural alignment and deconstruction of the kinase domains from&amp;nbsp;over 1734 PDB structures covering 190 different human kinases.&amp;nbsp;&lt;/p&gt;

&lt;p&gt;Every crystal structure was structurally aligned in a consistent manner, subsequently broken down from the full complex into separate structural parts: the protein, the orthosteric ligand-binding pocket (85 aligned residues covering the catalytic cleft), orthosteric and allosteric ligand(s), ions, organometallics, cofactors, and waters. By combining the pocket with the orthosteric ligand all interactions are annotated using Interactions FingerPrints (IFPs) for systematic comparison.&lt;/p&gt;</description>
    <description descriptionType="Other">This dataset is part of a 2013 publication in Journal of Medicinal Chemistry (doi: 10.1021/jm400378w). For the new, web-based, and automatically updated version of KLIFS please go to http://klifs.vu-compmedchem.nl as published in the 2016 database issue of Nucleic Acids Research (doi: 10.1093/nar/gkv1082).</description>
  </descriptions>
</resource>
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