Software Open Access

Dabble

Robin Betz


MARC21 XML Export

<?xml version='1.0' encoding='UTF-8'?>
<record xmlns="http://www.loc.gov/MARC21/slim">
  <leader>00000nmm##2200000uu#4500</leader>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">molecular dynamics, charmm, amber, lipid</subfield>
  </datafield>
  <controlfield tag="005">20171102115258.0</controlfield>
  <controlfield tag="001">836914</controlfield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">14363862</subfield>
    <subfield code="z">md5:940f35d0f7b3280eb234d686ac2290ba</subfield>
    <subfield code="u">https://zenodo.org/record/836914/files/Eigenstate/dabble-v2.6.3.zip</subfield>
  </datafield>
  <datafield tag="542" ind1=" " ind2=" ">
    <subfield code="l">open</subfield>
  </datafield>
  <datafield tag="260" ind1=" " ind2=" ">
    <subfield code="c">2017-08-01</subfield>
  </datafield>
  <datafield tag="909" ind1="C" ind2="O">
    <subfield code="p">software</subfield>
    <subfield code="o">oai:zenodo.org:836914</subfield>
  </datafield>
  <datafield tag="100" ind1=" " ind2=" ">
    <subfield code="u">Stanford University</subfield>
    <subfield code="a">Robin Betz</subfield>
  </datafield>
  <datafield tag="245" ind1=" " ind2=" ">
    <subfield code="a">Dabble</subfield>
  </datafield>
  <datafield tag="540" ind1=" " ind2=" ">
    <subfield code="u">http://www.opensource.org/licenses/GPL-2.0</subfield>
    <subfield code="a">GNU General Public License v2.0 only</subfield>
  </datafield>
  <datafield tag="650" ind1="1" ind2="7">
    <subfield code="a">cc-by</subfield>
    <subfield code="2">opendefinition.org</subfield>
  </datafield>
  <datafield tag="520" ind1=" " ind2=" ">
    <subfield code="a">&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;</subfield>
  </datafield>
  <datafield tag="773" ind1=" " ind2=" ">
    <subfield code="n">url</subfield>
    <subfield code="i">isSupplementTo</subfield>
    <subfield code="a">https://github.com/Eigenstate/dabble/tree/v2.6.3</subfield>
  </datafield>
  <datafield tag="773" ind1=" " ind2=" ">
    <subfield code="n">doi</subfield>
    <subfield code="i">isVersionOf</subfield>
    <subfield code="a">10.5281/zenodo.836913</subfield>
  </datafield>
  <datafield tag="024" ind1=" " ind2=" ">
    <subfield code="a">10.5281/zenodo.836914</subfield>
    <subfield code="2">doi</subfield>
  </datafield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">software</subfield>
  </datafield>
</record>
196
17
views
downloads
All versions This version
Views 196196
Downloads 1717
Data volume 244.2 MB244.2 MB
Unique views 186186
Unique downloads 1111

Share

Cite as