[ssml] MLE

[Kevin Karplus]

Yes, the family pairwise search by Bill Grundy (now William Noble) is
an interesting and fairly simple technique for trying to improve
homology detection by using known relationships among sequences in the
database.  I've had students implement Grundy's "product of p-values"
technique for our HMM-based scoring methods.  In their preliminary
tests, they showed that it might help, but their projects were never
taken to the point where the method could be incorporated into an
automatic prediction method.  

One problem with that method is that it treats all templates in a fold
class as equally informative and does not use information from
templates in competing fold classes.  One can envision combining
methods such as logisitic regression that could use the extra
information to get better predictions.  One danger is that
multi-domain proteins correctly have multiple correct folds, so simple
competition between fold classes is not quite the right model.

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Kevin Karplus 	karplus at soe.ucsc.edu	http://www.soe.ucsc.edu/~karplus
Senior member, IEEE	Board of Directors, ISCB (starting Jan 2005)
Professor of Biomolecular Engineering, University of California, Santa Cruz
Undergraduate and Graduate Director, Bioinformatics
Affiliations for identification only.