Appropirate Usage of TMBpro
TMBpro assumes that the sequence is for a TMB protein. TMBpro does not contain
a screening component or predict the probability that a given protein really is
a TMB protein. It is a specialized predictor and not a general purpose tertiary structure predictor.
For any protein you submit, including globular, TMBpro will predict the secondary structure, contacts,
and then build a model utilizing available TMB templates. If the protein is not a TMB protein then
the model is destined to be wrong. To use TMBpro appropriately you should first have some evidence
that your sequence is a TMB protein.
TMB Screening Methods
A variety of methods have been developed for discriminating TMB from non-TMB proteins.
We have confirmed the following methods were functioning as of 11-24-2008:
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PRED-TMBB
Bagos,P. et al. (2004) Nucleic Acids Res., 32, W400-W404.
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TMB-HUNT
Garrow,A. et al. (2005) Nucleic Acids Res., 33, W188-W192.
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TMBETA-NET
Gromiha,M. et al. (2005) Nucleic Acids Res., 33, W164-W167.
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Beta-Barrel Finder
Zhai.Y and Saier,M. (2002) Protein Sci., 11, 2196-2207.
Contact TMBpro Administrator: arandall@ics.uci.edu
Institute for Genomics and Bioinformatics
School of Information & Computer Science
University of California Irvine
