MEMSAT predicts 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.
MEMSAT3 predicting transmembrane protein topology from sequence profiles On a standard data set of 184 transmembrane proteins the method was found to predict both the correct topology and the locations of transmembrane segments for 80% of the test set.
Also, by using a second neural network specifically to discriminate transmembrane from globular proteins, a very low overall false positive rate (0.5%) was achieved in detecting transmembrane proteins.
The system has user adjustable parameters that can be set appropriately. For instance if you already know that your protein is a transmembrane protein you can concentrate on the predicted locations and topology in more detail.
See the following for more information:
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
About the image on this banner
The image used here was sourced from a set of membrane images provided by pixabay under CC0