Online tools for predicting integral membrane proteins.

TitleOnline tools for predicting integral membrane proteins.
Publication TypeJournal Article
Year of Publication2009
AuthorsBigelow, H, Rost, B
JournalMethods Mol Biol
Date Published2009
KeywordsComputational Biology, Computer Simulation, Databases, Protein, Membrane Proteins, Models, Molecular, Protein Structure, Secondary, Sequence Analysis, Protein, Software, Structural Homology, Protein

We identify and describe a set of tools readily available for integral membrane protein prediction. These tools address two problems: finding potential transmembrane proteins in a pool of new sequences, and identifying their transmembrane regions. All methods involve comparing the query protein against one or more target models. In the simplest of these, the target "model" is another protein sequence, while the more elaborate methods group together the entire set of t ansmembrane helical or transmembrane beta-barrel proteins. In general, prediction accuracy either in identifying new integral membrane proteins or transmembrane regions of known integral membrane proteins depends strongly on how closely the query fits the model. Because of this, the best approach is an opportunistic one: submit the protein of interest to all methods and choose the results with the highest confidence scores.

Alternate JournalMethods Mol. Biol.
PubMed ID19153681
Grant ListR01-LM07329-01 / LM / NLM NIH HHS / United States