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Department of Physiology and Biophysics and the Program in Structural Biology, University of California, Irvine, California 92697–4560, USA
Reprint requests to: Dr. Stephen H. White, University of California at Irvine, Department of Physiology and Biophysics, Irvine, California 92697–4560, USA; e-mail: shwhite{at}uci.edu; fax: (949) 824-8540.
The reliability of the transmembrane (TM) sequence assignments for membrane proteins (MPs) in standard sequence databases is uncertain because the vast majority are based on hydropathy plots. A database of MPs with dependable assignments is necessary for developing new computational tools for the prediction of MP structure. We have therefore created MPtopo, a database of MPs whose topologies have been verified experimentally by means of crystallography, gene fusion, and other methods. Tests using MPtopo strongly validated four existing MP topology-prediction algorithms. MPtopo is freely available over the internet and can be queried by means of an SQL-based search engine.
Keywords: Protein structure prediction; prediction accuracy; hydropathy plots
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