Abstract
Biological analysis of segment formation in Drosophila embryogenesis provides a good ground for modelling interaction of DNA-binding proteins. In this paper, we propose threshold model for qualitative simulation of the interaction, and introduce SIMFLY2. This revised version of SIMFLY, a simulator for protein interaction, integrates genetic algorithm for the search of optimal relations among proteins. We confirmed that SIMFLY2 did find the relation we had found last time in SIMFLY by exhaustive search. SIMFLY2 also found interaction models between two pair-rule proteins and gap proteins.
