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. 2001 Feb;10(2):455-8.
doi: 10.1110/ps.43501.

MPtopo: A database of membrane protein topology

S Jayasinghe  1 , K Hristova, S H White
Affiliations

MPtopo: A database of membrane protein topology

S Jayasinghe et al. Protein Sci. 2001 Feb.

Abstract

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.

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Figures

Fig. 1.
Fig. 1.
Web tools for using MPtopo. (A) MPtopo Querier, a java applet designed to search the MPtopo database using an SQL-based server. With Querier, MPtopo may be searched by protein name, authors, number of transmembrane (TM) segments, Protein Information Resource (PIR) identifier, Protein Data Bank (PDB) identifier, or any combination of these fields. The search can be performed on the whole MPtopo database or limited to one of the subsets. MPtopo Querier is available for use over the World Wide Web from our Web site at http://blanco.biomol.uci.edu/mptopo. (B) Search results from Querier are displayed within the results window. Each returned result is displayed as the complete database entry. Each entry contains 15 fields including the complete protein sequence, the number of transmembrane (TM) segments, TM segment start and end positions, PIR and PDB identifiers (when available), a complete reference citation, and the topology (Nterm = in or out). Selected entries may be sent to MPEx, a hydropathy plot TM segment prediction tool developed in our laboratory (S. Jayasinghe, K. Hristova, and S.H. White, in prep.). The complete database is also available for anonymous ftp download as a plain text file at blanco.biomol.uci.edu/mptopo.
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References

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