Online prediction of interacting proteins with a user-specified protein

Abstract

The protein-protein interaction data available today in databases were either determined by experimental methods or predicted by computational methods. Biologists studying a certain mechanism or function are usually interested in a small-scale network of protein-protein interactions related to the mechanism or function of their interest rather than a genome-wide network of protein-protein interactions. We have previously developed a database server that can predict interactions between the proteins submitted by a user. However, the server cannot find proteins from the databases that potentially interact with a protein given by a user. Finding potentially interacting proteins with a protein of interest is more useful than finding interactions between given proteins, but more difficult partly because it involves intensive computation of searching data in the databases and because different databases have different accession numbers and names for a same protein. This paper describes the new online system for predicting interacting proteins with a user-specified human protein and its preliminary results. We believe that this is the first online system for predicting interacting proteins with a given protein and that it is a useful resource for studying protein-protein interactions. © Springer-Verlag Berlin Heidelberg 2005.