Bioinformatics tools & analysis of protein structure and function

This dissertation mainly focuses on protein structure and functional studies from the viewpoint of Bioinformatics. My dissertation consists of three bioinformatics projects, which all utilized bioinformatics tools to understand the structure and function of proteins. The first project introduced an optimal strategy to identify optimal mutation sites in NMR experiments, and to predict trans-membrane proteins topology with minimum number of PRE sites. The second project is to develop a novel template based structure prediction tool using segmental structure instead of whole chain structure. The structural segments could help to identify the proteins of novel structures without proper templates. In the last project, I applied multiple bioinformatics tools to model the structure of a protein complex, ferredoxin hydrogenase in Thermotoga maritima. The model structure gives a new perspective on our understanding of the redox proteins and mechanism of H2 production in anaerobic bacteria.