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A Rule-Based Model of Base Excision Repair

  • Agnes Köhler
  • Jean Krivine
  • Jakob Vidmar
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8859)

Abstract

There are ongoing debates in the DNA repair community on whether the coordination of DNA repair is achieved by means of direct protein-protein interactions or whether substrate specificity is sufficient to explain how DNA intermediates are channeled from one repair enzyme to the other. In order to address these questions we designed a model of the Base Excision Repair pathway in Kappa, a rule based formalism for modeling protein-protein and protein-DNA interactions. We use this model to shed light on the key role of the scaffolding protein XRCC1 in coordinating the repair process.

Keywords

Base Excision Repair Nucleic Acid Research Base Excision Repair Pathway Cytotoxic Substrate Base Excision Repair Enzyme 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Agnes Köhler
    • 1
  • Jean Krivine
    • 2
  • Jakob Vidmar
    • 2
  1. 1.Domaine de Voluceau - RocquencourtINRIA-RocquencourtLe ChesnayFrance
  2. 2.Laboratoire PPS, UMR 7126Univ. Paris Diderot, Sorbonne Paris CitéParisFrance

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