March 4, 2020 Dataset Open Access

Raniolo, Stefano; Limongelli, Vittorio

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  <identifier identifierType="DOI">10.5281/zenodo.3697115</identifier>
  <creators>
    <creator>
      <creatorName>Raniolo, Stefano</creatorName>
      <givenName>Stefano</givenName>
      <familyName>Raniolo</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-4835-8696</nameIdentifier>
      <affiliation>Università della Svizzera Italiana</affiliation>
    </creator>
    <creator>
      <creatorName>Limongelli, Vittorio</creatorName>
      <givenName>Vittorio</givenName>
      <familyName>Limongelli</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-4861-1199</nameIdentifier>
      <affiliation>Università della Svizzera Italiana</affiliation>
    </creator>
  </creators>
  <titles>
    <title>FMAP data files</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2020</publicationYear>
  <subjects>
    <subject>ligand binding mode</subject>
    <subject>ligand binding free energy</subject>
    <subject>molecular docking</subject>
    <subject>molecular dynamics</subject>
    <subject>funnel-metadynamics</subject>
    <subject>enhanced sampling</subject>
    <subject>free-energy calculations</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2020-03-04</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/3697115</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.3697114</relatedIdentifier>
  </relatedIdentifiers>
  <version>1.00</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;The accurate study of the binding mechanism of a ligand to its molecular target is fundamental to discover new possible drug targets. In order to do that, we can employ free-energy calculations&amp;nbsp;due to their accuracy, although&amp;nbsp;the&amp;nbsp;lack in&amp;nbsp;user-friendliness&amp;nbsp;generally&amp;nbsp;hampers&amp;nbsp;their&amp;nbsp;broad application.&amp;nbsp;&lt;/p&gt;

&lt;p&gt;In this regard, the Funnel-Metadynamics Advanced Protocol (FMAP) represents a flexible and user-friendly protocol to perform Funnel-Metadynamics, a binding free-energy method that employs a funnel-shape restraint potential to obtain the ligand binding mode and the accurate calculation of the absolute ligand/protein binding free energy. Through the use of graphical interfaces, FMAP is able to assist the user during all steps of the investigation, allowing to disclose the ligand binding mode and mechanism and accurately compute the absolute protein/ligand binding free energy.&lt;/p&gt;

&lt;p&gt;This package contains inputs and outputs files&amp;nbsp;of FMAP&amp;nbsp;produced for the paradigmatic benzamidine-trypsin system.&lt;/p&gt;</description>
    <description descriptionType="Other">We would like to acknowledge the support of the Italian MIUR-PRIN 2017 (project id 2017FJZZRC) and the Swiss National Supercomputing Centre (CSCS) [project ID u8].</description>
  </descriptions>
  <fundingReferences>
    <fundingReference>
      <funderName>Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100001711</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/SNSF/Project+funding/200021_163281/">200021_163281</awardNumber>
      <awardTitle>Extensive computer simulations investigate TPP1-TERT protein-protein interaction</awardTitle>
    </fundingReference>
  </fundingReferences>
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