We are working on developing approaches to bridge between protein structures and biochemical networks, from the molecular to the cellular level.
We have recently released LigDig, a webserver for querying ligand-protein interactions. It has been designed to assist users in systems biology projects with queries that require access to multiple data sources as well as basic manipulations of the structures of protein-ligand complexes, and can be used together with SYCAMORE (SYstems biology’s Computational Analysis and MOdeling Research Environment).
In the Human Brain Project, we are contributing to the development of multi-scale molecular simulation techniques for the brain simulation platform.
In the Sysmolab (Comparative systems biology of lactic acid bacteria) projects, we have explored how differences in the allosteric regulation of key metabolic enzymes can be related to differences in the environment in which the bacteria live (Feldman-Salit, 2013; Veith, 2013). These studies made use of our PIPSA (Protein Interaction Property Similarity Analysis) webserver and software.