A Rule-Based Model of Base Excision Repair

Agnes Köhler (1) , Jean Krivine (1) , Jakob Vidmar (1)

1 PPS - Preuves, Programmes et Systèmes

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.

Domaines: Modélisation et simulation; Bio-Informatique, Biologie Systémique [q-bio.QM]; Cancer

Agnes Köhler, Jean Krivine, Jakob Vidmar. A Rule-Based Model of Base Excision Repair. Computational Methods in Systems Biology, Nov 2014, Manchester, United Kingdom. pp.173 - 195, ⟨10.1007/978-3-319-12982-2_13⟩. ⟨hal-01107691⟩