Scalable rule-based modelling of allosteric proteins and biochemical networks.

ABSTRACT: Much of the complexity of biochemical networks comes from the information-processing abilities of allosteric proteins, be they receptors, ion-channels, signalling molecules or transcription factors. An allosteric protein can be uniquely regulated by each combination of input molecules that it binds. This "regulatory complexity" causes a combinatorial increase in the number of parameters required to fit experimental data as the number of protein interactions increases. It therefore challenges the creation, updating, and re-use of biochemical models. Here, we propose a rule-based modelling framework that exploits the intrinsic modularity of protein structure to address regulatory complexity. Rather than treating proteins as "black boxes", we model their hierarchical structure and, as conform

SUBMITTER: Ollivier JF 

PROVIDER: S-EPMC2973810 | biostudies-literature | 2010 Nov

REPOSITORIES: biostudies-literature