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MEMSAT3 - MEMbrane protein Structure And Topology.

MEMSAT3 is a program which predicts the secondary structure and topology of all-helix integral membrane proteins based on the recognition of topological models. The original MEMSAT method employed a set of statistical tables (log likelihood ratios) compiled from well- characterized membrane protein data, and a novel dynamic programming algorithm to recognize membrane topology models by expectation maximization. These statistical tables showed definite biases towards certain amino acid species on the inside, middle and outside of a cellular membrane.

MEMSAT3 was released in January 2007 and now employs a neural network to determine which residues are on the cytoplasmic side of the membrane and which residues are within transmembrane helices. The same dynamic programming algorithm is used to calculate the most likely overall topology.

The newest method is described in the following reference:

Jones D.T. (2007) Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics. In press. PUBMED

The original method is described in the following reference:

Jones, D.T., Taylor, W.R. and Thornton, J. M. (1994) Biochemistry. 33:3038-3049. PUBMED

MEMSAT3 can be run from the PSIPRED prediction server or MEMSAT3 source code can be downloaded from HERE.

COMMERCIAL USERS SHOULD CONSULT THE README FILE FOR LICENSING DETAILS BEFORE DOWNLOADING THIS SOFTWARE.