Web Service for Predicting Interacting Proteins and Application to Human and HIV-1 Proteins

Abstract

Finding all the proteins that potentially interact with a query protein is useful when studying a biological mechanism, but it is much more difficult than finding interactions between a set of given proteins. This is because it involves intensive computation to search the relevant data in databases, and different databases have different accession numbers and names for the same protein. Recently a few servers have been developed for finding interactions between user-specified proteins, but none of these can find all the potentially interacting proteins for a given protein, including the former version of our prediction server, HPID version 1.0. This paper describes a new online prediction system, HPID 2.0 (http://www.hpid.org), for finding partners interacting with a query protein as well as for finding interactions between query proteins. We applied the new system to predicting the interactions between the entire human proteins, and to identifying human proteins interacting with HIV-1 proteins (http://hiv1.hpid.org). We believe that this is the first online server for predicting proteins interacting with a given protein, and that it will be a useful resource for studying protein-protein interactions.