MPtopo: A database of membrane protein topology

The reliability of the transmembrane (TM) sequence assignments for membrane proteins (MPs) in standard sequence databases is uncertain because the vas t majority are based on hydropathy plots. A database of MPs with dependable assignments is necessary for developing new computational tools for the pr ediction of MP structure. We have therefore created MPtopo, a database of M Ps whose topologies have been verified experimentally by means of crystallo graphy, gene fusion, and other methods. Tests using MPtopo strongly validat ed four existing MP topology prediction algorithms. MPtopo is freely availa ble over the internet and can be queried by means of an SQL-based search en gine.