Prısm : protein arayüzlerinin sorgulanması, incelenmesi, ve görselleştirilmesi için bir sistem

Many biological processes in the cell are carried out by a complex network of interactions amongnumerous proteins. The ultimate goal of computational biology would be to simulate this extremelycomplex machinery called the cell, using in silico methods. In that sense, binary interactions occurringat the atomic level between individual proteins are the building blocks of biological networks. Today,there are many experimental and computational methods used extensively for the generation of proteininteraction data. However, one important source of interactions is often overlooked: proteincomplexes. Here, we present PRISM, our software system used for the query, visualization andanalysis of protein interfaces obtained from protein complexes of known structures. Starting with thedataset of protein interfaces and a list of similar proteins to those interfaces, all relevant informationabout them are collected in a relational database. The content of the database is made availablethrough our website. The design of the website also incorporates additional on-line tools used for thepurpose of exploring protein interfaces. An interaction map is generated using the pairwise similaritydata. In addition, a graphical tool is developed which can be used for the visualization and explorationof interaction data. We have used the data stored in our database to extract some biologically relevantinferences about protein interfaces, and to perform a graph theoretic analysis of protein interactionnetworks.