Journal article Open Access

Machine Learning Analysis of τRAMD Trajectories to Decipher Molecular Determinants of Drug-Target Residence Times

Daria B. Kokh; Tom Kaufmann; Bastian Kister; Rebecca C. Wade


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  <identifier identifierType="DOI">10.5281/zenodo.3522753</identifier>
  <creators>
    <creator>
      <creatorName>Daria B. Kokh</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-4687-6572</nameIdentifier>
      <affiliation>HITS gGmbH</affiliation>
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    <creator>
      <creatorName>Tom Kaufmann</creatorName>
      <affiliation>HITS gGmbH, Heidelberg University</affiliation>
    </creator>
    <creator>
      <creatorName>Bastian Kister</creatorName>
      <affiliation>HITS gGmbH, Heidelberg University</affiliation>
    </creator>
    <creator>
      <creatorName>Rebecca C. Wade</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-5951-8670</nameIdentifier>
      <affiliation>HITS gGmbH, Heidelberg University</affiliation>
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  </creators>
  <titles>
    <title>Machine Learning Analysis of τRAMD Trajectories to Decipher Molecular Determinants of Drug-Target Residence Times</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2019</publicationYear>
  <subjects>
    <subject>Machine Learning</subject>
    <subject>tauRAMD</subject>
    <subject>drug-protein residence time</subject>
    <subject>structure-kinetic relationship (SKRs)</subject>
    <subject>drug-target binding kinetics</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2019-03-27</date>
  </dates>
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    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsCitedBy" resourceTypeGeneral="JournalArticle">10.3389/fmolb.2019.00036</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.2611620</relatedIdentifier>
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  <version>2.3</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>
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  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;The manuscript, supporting data and codes for the manuscript:&lt;/p&gt;

&lt;p&gt;&amp;quot;Machine learning analysis of tauRAMD trajectories to decipher molecular determinants of drug-target residence times&amp;quot; of&amp;nbsp; Kokh DB, Kaufman T, Kister B, Wade RC., Front. Mol. Biosci., 24 May 2019 | &lt;a href="https://doi.org/10.3389/fmolb.2019.00036"&gt;https://doi.org/10.3389/fmolb.2019.00036&lt;/a&gt;&lt;/p&gt;

&lt;p&gt;&lt;a href="https://zenodo.org/api/files/81bc9d41-936a-41b2-9a55-fc167f9f476f/fmolb-06-00036.pdf?versionId=a85dc17f-6e49-4cd8-88db-368db5d3e300"&gt;fmolb-06-00036.pdf&amp;nbsp; &lt;/a&gt;- paper&lt;br&gt;
&lt;a href="https://zenodo.org/api/files/81bc9d41-936a-41b2-9a55-fc167f9f476f/HSP90.tar.gz"&gt;HSP90.tar.gz&amp;nbsp; &lt;/a&gt;- topology and coordinate files for all&amp;nbsp; complexes used in RAMD simulations&lt;/p&gt;

&lt;p&gt;&lt;a href="https://zenodo.org/api/files/81bc9d41-936a-41b2-9a55-fc167f9f476f/ML-HSP90-v2.1.tar.gz?versionId=4d8856a1-5ca4-4f70-9dd3-bf6e63107cc6"&gt;ML-HSP90-v2.1.tar.gz&amp;nbsp; &lt;/a&gt;- scripts and input data for ML analysis of ligand dissociation reported in the paper&lt;br&gt;
&lt;br&gt;
&amp;nbsp;&lt;/p&gt;</description>
  </descriptions>
  <fundingReferences>
    <fundingReference>
      <funderName>European Commission</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000780</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/EC/H2020/785907/">785907</awardNumber>
      <awardTitle>Human Brain Project Specific Grant Agreement 2</awardTitle>
    </fundingReference>
    <fundingReference>
      <funderName>European Commission</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000780</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/EC/FP7/211528/">211528</awardNumber>
      <awardTitle>Partnership for Advanced Computing in Europe</awardTitle>
    </fundingReference>
    <fundingReference>
      <funderName>European Commission</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000780</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/EC/FP7/115366/">115366</awardNumber>
      <awardTitle>Kinetics for Drug Discovery (K4DD)</awardTitle>
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