In the Post-genomic era the focus of research in molecular biology is shifting towards analysis of voluminous data collected by high-througput and classical experimental approaches. The ultimate goal of these studies is to understand how the behavior of the cell emerges as the result of interaction among its molecular components. Due to the amount of experimental data and complexity of underlying system, understanding the cell in terms of molecular interactions is a paramount task. This goal can be achieved only by community effort of interdisciplinary research teams applying variety of theoretical approaches to the analysis of publicly available experimental data. The task of our group is to participate in this effort. We have expertise in the application of classical bioinformatic methods, mainly in the area of comparative analysis of protein sequences and structures. We are also working in the emerging field of Systems Biology and focusing on the dynamics of biochemical reaction networks. We develop the STOCKS software for the stochastic kinetic simulations of biochemical systems. We frequently collaborate with experimental groups.