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Dabble

Robin Betz


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  <identifier identifierType="DOI">10.5281/zenodo.836914</identifier>
  <creators>
    <creator>
      <creatorName>Robin Betz</creatorName>
      <affiliation>Stanford University</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Dabble</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2017</publicationYear>
  <subjects>
    <subject>molecular dynamics, charmm, amber, lipid</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2017-08-01</date>
  </dates>
  <resourceType resourceTypeGeneral="Software"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/836914</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsSupplementTo">https://github.com/Eigenstate/dabble/tree/v2.6.3</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.836913</relatedIdentifier>
  </relatedIdentifiers>
  <version>v2.6.3</version>
  <rightsList>
    <rights rightsURI="http://www.opensource.org/licenses/GPL-2.0">GNU General Public License v2.0 only</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;Dabble is a tool for building membrane protein systems. The ultimate goal of the project is to create an easy to use, one stop tool for system construction and parameterization.&lt;/p&gt;

&lt;p&gt;Some uses for Dabble:&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;Prepare membrane protein systems by inserting them into a membrane&lt;/li&gt;
	&lt;li&gt;Prepare solvated proteins by adding water&lt;/li&gt;
	&lt;li&gt;Add ions to neutralize and/or to desired concentration&lt;/li&gt;
	&lt;li&gt;Parameterize with CHARMM or AMBER parameter sets&lt;/li&gt;
	&lt;li&gt;Outputs files for simulation with AMBER or CHARMM&lt;/li&gt;
	&lt;li&gt;Automatic detection of post-translational modifications&lt;/li&gt;
	&lt;li&gt;Modified amino acids made easy&lt;/li&gt;
	&lt;li&gt;Ligands made easy! No more messing with atom names.&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;Dabble can use CHARMM or AMBER parameters, and generate input files for simulating in NAMD, CHARMM, Anton, or Desmond. While Dabble can be run from the command-line, it also provides a powerful API for building and parameterizing systems.&lt;/p&gt;

&lt;p&gt;Dabble's full documentation is available at http://dabble.robinbetz.com&lt;/p&gt;</description>
  </descriptions>
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