1 Ocak 2016 Dergi makalesi Açık Erişim

Soylu, Inanc; Marino, Stefano M.

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  <identifier identifierType="URL">https://aperta.ulakbim.gov.tr/record/55833</identifier>
  <creators>
    <creator>
      <creatorName>Soylu, Inanc</creatorName>
      <givenName>Inanc</givenName>
      <familyName>Soylu</familyName>
      <affiliation>Akdeniz Univ, Dept Agr Biotechnol, TR-07058 Antalya, Turkey</affiliation>
    </creator>
    <creator>
      <creatorName>Marino, Stefano M.</creatorName>
      <givenName>Stefano M.</givenName>
      <familyName>Marino</familyName>
      <affiliation>Akdeniz Univ, Dept Agr Biotechnol, TR-07058 Antalya, Turkey</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Cy-Preds: An Algorithm And A Web Service For The Analysis And Prediction Of Cysteine Reactivity</title>
  </titles>
  <publisher>Aperta</publisher>
  <publicationYear>2016</publicationYear>
  <dates>
    <date dateType="Issued">2016-01-01</date>
  </dates>
  <resourceType resourceTypeGeneral="Text">Journal article</resourceType>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://aperta.ulakbim.gov.tr/record/55833</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsIdenticalTo">10.1002/prot.24978</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="http://www.opendefinition.org/licenses/cc-by">Creative Commons Attribution</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
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  <descriptions>
    <description descriptionType="Abstract">Cysteine (Cys) is a critically important amino acid, serving a variety of functions within proteins including structural roles, catalysis, and regulation of function through post-translational modifications. Predicting which Cys residues are likely to be reactive is a very sought after feature. Few methods are currently available for the task, either based on evaluation of physicochemical features (e.g., pKa and exposure) or based on similarity with known instances. In this study, we developed an algorithm (named HAL-Cy) which blends previous work with novel implementations to identify reactive Cys from nonreactive. HAL-Cy present two major components: (i) an energy based part, rooted on the evaluation of H-bond network contributions and (ii) a knowledge based part, composed of different profiling approaches (including a newly developed weighting matrix for sequence profiling). In our evaluations, HAL-Cy provided significantly improved performances, as tested in comparisons with existing approaches. We implemented our algorithm in a web service (Cy-preds), the ultimate product of our work; we provided it with a variety of additional features, tools, and options: Cy-preds is capable of performing fully automated calculations for a thorough analysis of Cys reactivity in proteins, ranging from reactivity predictions (e.g., with HAL-Cy) to functional characterization. We believe it represents an original, effective, and very useful addition to the current array of tools available to scientists involved in redox biology, Cys biochemistry, and structural bioinformatics.</description>
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