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Project files provided as supporting information to the manuscript "An information theory-based approach for optimal model reduction of biomolecules"

Marco Giulini; Roberto Menichetti; Raffaello Potestio


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  <identifier identifierType="DOI">10.5281/zenodo.3776293</identifier>
  <creators>
    <creator>
      <creatorName>Marco Giulini</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-2691-712X</nameIdentifier>
      <affiliation>University of Trento</affiliation>
    </creator>
    <creator>
      <creatorName>Roberto Menichetti</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-5961-6438</nameIdentifier>
      <affiliation>University of Trento</affiliation>
    </creator>
    <creator>
      <creatorName>Raffaello Potestio</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-6408-9380</nameIdentifier>
      <affiliation>University of Trento</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Project files provided as supporting information to the manuscript "An information theory-based approach for optimal model reduction of biomolecules"</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2020</publicationYear>
  <dates>
    <date dateType="Issued">2020-04-29</date>
  </dates>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/3776293</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.3776292</relatedIdentifier>
  </relatedIdentifiers>
  <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 dataset contains the following files:&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;- adenylate.zip&lt;/li&gt;
	&lt;li&gt;- antitrypsin.zip&lt;/li&gt;
	&lt;li&gt;- tamapin.zip&lt;/li&gt;
	&lt;li&gt;- analysis_notebooks.zip&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;Each of these refers to one of three proteins. For each CG sites number N, each compressed folder contains the following files:&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;random mappings (random_mappings_${N}.txt)&amp;nbsp;&lt;/li&gt;
	&lt;li&gt;random mapping entropies (random_smaps_${N}.txt) [fig1]&lt;/li&gt;
	&lt;li&gt;optimal mappings (lowest_mappings_${N}.txt) [fig3, fig4, figS2]&lt;/li&gt;
	&lt;li&gt;optimal mapping entropies (lowest_smaps_${N}.txt) [fig1]&lt;/li&gt;
	&lt;li&gt;pdb files with conservations probabilities in the beta factor column (${N}_probs.pdb) [fig4, figs2]&lt;/li&gt;
	&lt;li&gt;SASA values (${protein_name}_SASA_residues.xvg&amp;nbsp;&lt;/li&gt;
	&lt;li&gt;transition mapping entropies (${protein_name}_transition_smaps.txt) [fig2]&lt;/li&gt;
	&lt;li&gt;additional transition mapping entropies (${protein_name}_transition_smaps*) [figs3]&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;The file&amp;nbsp;analysis_notebooks.zip contains the python3 notebooks employed to perform all the analysis present in the paper:&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;paper_analysis_adenylate.ipynb&lt;/li&gt;
	&lt;li&gt;paper_analysis_antitrypsin.ipynb&lt;/li&gt;
	&lt;li&gt;paper_analysis_tamapin.ipynb&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;Packages required for the usage of these python 3 scripts:&lt;/p&gt;

&lt;p&gt;- numpy&lt;br&gt;
- pandas&lt;br&gt;
- matplotlib&lt;br&gt;
- seaborn&lt;br&gt;
&amp;nbsp;&lt;/p&gt;</description>
  </descriptions>
  <fundingReferences>
    <fundingReference>
      <funderName>European Commission</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/100010661</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/EC/H2020/758588/">758588</awardNumber>
      <awardTitle>VAriable ResolutIon Algorithms for macroMOLecular Simulation</awardTitle>
    </fundingReference>
  </fundingReferences>
</resource>
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