[BiO BB] Protein fold prediction

[Dennis Livesay]

Hello all,

I'm trying to determine the best (threading) software for a large scale,
multiple proteome fold prediction study.  We have two competing factors that I
have to consider...  (1) We're especially interested in sequences with little
homology to others, but (2) due to the size of our dataset, we need software
that is robust and requires little human involvement.

>From a cursory assesment of the available software, it appears that PROSPECT
meets the first requirement, but doesn't do as well with the second.  On the
other hand, 3D-PSSM or 123D seem to be the opposite.  Any advice???

Thanks in advance,
Dennis

--------------------------------------------------------------------
Dr. Dennis Livesay
Department of Chemistry
Cal Poly, Pomona
phone: 909-869-4409
email: drlivesay at csupomona.edu
http://www.csupomona.edu/~drlivesay/