Research Group M.J. Sippl

Research at the Center of Applied Molecular Engineering (CAME) is focused on the three-dimensional structure of proteins and the classical protein folding problem, i.e. how to calculate the 3D structure of a protein from its amino acid sequence. To tackle this problem, CAME pursues the successful approach to derive the rules for protein folding from experimentally determined protein structures. In essence, the results are force fields (so-called potentials of mean force) that are used to calculate and predict the 3D structure of proteins. An important area of application of these potentials is the method of fold recognition, which allows for predicting a protein structure even in cases if there are no experimental data for the protein except its amino acid sequence. Further applications are the recognition of errors in experimentally determined protein structures, the refinement of structure models and the computer-aided assessment of protein mutants for the design of proteins with desired properties.

A further main research topic at CAME is the characterization of similarities between proteins and the closely connected problem of protein classification. The question of how similarities between proteins can be defined and determined plays a central role in protein evolution research and tools that can reliably detect structural similarities between proteins are among the most valuable in bioinformatics. Based on their similarities proteins are grouped into families that can be used to derive so-called profiles. Such profiles provide an important means to search for novel members of a protein family which in turn are often of medical relevance.

It is a tradition at CAME to make its programs accessible to the academic world. Among the CAME tools widely used by researchers are ProSA (a computer program for the analysis of protein structures), NQ-Flipper (an online service for the recognition of erroneous asparagine and glutamine rotamers in protein structures) and QSCOP (an online service for the identification of structural relationships among protein domains).