SYCAMORE: SYstems biology’s Computational Analysis and MOdeling Research Environment
The
aim of the SYCAMORE project is to develop a system of software tools
and computational methods to support concerted computational and
experimental approaches to systems biology problems. The project
is a collaboration between the BCB and MCM groups at EML Research. It
is part of the Modeling Platform of the 'Hepatosys' BMBF Systems Biology programme.
The MCM group is working on the development and application of
methods to harness protein structural information for systems biology
projects. One example of how this can be achieved is provided by a
recent study together with Ursula Kummer (BCB group, EML Research)
and Lars Olsen (Odense, Denmark) in which concerted use was made
of biochemical network simulations and protein structure-based
simulations to reveal how peroxidase compound III formation results in
cellular oscillations (Gabdoulline et al, 2003). Currently, we are developing the qPIPSA approach to estimate kinetic parameters from protein interaction fields (Stein et al, 2006)(Stein et al, 2007).
