Bioinformatic analysis and molecular modeling have a potential of becoming particularly important tools in protein engineering and drug discovery by systematic analysis and study of the ever increasing volumes of protein sequences and 3D-structures attributed to functionally diverse superfamilies. The common problem of many programs/algorithms in computational biology is that they were advertised as helpful tools to assist experimental studies, but usually required profound skills in computational biology, what impeded practical use by many investigators in a daily laboratory practice. Our goal is to provide advanced computational methods directly to the wet-lab scientists by developing easy-to-use tools featuring content-rich interactive (on-line) output. This web-site features our new algorithms and automatized computational strategies in the field of bioinformatics and molecular modeling to study the mechanisms of protein function, design novel enzymes with improved properties and modulators of activity of the wild-type proteins.