Prısm 2.0: Prism'in iyileştirilmesi ve protein - protein etkileşimlerinin yapısal modellenmesini yapan bir internet sunucusunun tasarlanmasi

Biological processes in the cell mainly are carried out by protein – protein interaction networks among numerous proteins. One of the goals of the computational biology is to use mainly computational methods to predict interaction among proteins and understand how a cell functions. Today, there are many experimental and computational approaches used extensively to generate protein interaction data. One of the pioneer computational tools is PRISM. PRISM is the first template based protein – protein interaction prediction tool developed. PRISM has proven its success at many publications and used widely for prediction and structural modeling of protein-protein interactions as a stand-alone tool. However, its application to pathways, a network of protein-protein interactions, has both performance and usability limitations. In this thesis, a new version of PRISM (PRISM2.0) has been designed and implemented to make it efficient and easy-to-use for network of proteins predictions. PRISM2.0 is built from loosely coupled modules, therefore it is easy to use and develop further. A web server version of PRISM2.0 has been developed to create a protein–protein interaction repository. As the repository grows, it is expected to be a rich resource for protein-protein interactions. Users can enjoy using the web server without any installation or any further information about computer world rather than browsing the web page. We believe these tools will be beneficial for the community who is interested structural modeling of biological pathways.