A database of synaptic protein-protein interactions in rule-based format

The study of Protein-Protein interactions (PPI) involves the analysis and identification of protein complexes that may form under a variety of reaction conditions. Interacting biomolecules have the potential to interact in a myriad of different ways as the number of possible post-translational modifications grow exponentially when considering the binary interactions within the reaction network. Using traditional methods like ODEs requires large amounts of reaction specific details, which sets the limitation on the size of the modelled system. A rule-based model, on the other hand, comprises of a set of rules where the network specification is implicit, which allows to model large-scale protein complexes. For this, PPIs should be defined using rule-based specification languages like Kappa (1) or BioNetGen (2). Respective software tools enable further simulation of those rules in deterministic or stochastic way. Up to date, thousands of synaptic PPIs are identified and plenty of rule-based model are published, while no existing database stores the Protein-Protein interaction rules. The purpose of this project is to create and load a database with synaptic PPIs in a rule-based format to enable researchers to reuse the existing models and create new models on demand.