Jaritz M., Domingues F., Floeckner H. and Sippl M.
Markus JARITZ Center for Applied Molecular Engineering University of
Salzburg Jakob Haringer Strasse 1 5020 SALZBURG AUSTRIA

We analyzed the quality of predictions made by ProFIT1 using several
target sequences of known structure. The ProFIT user did not know in
advance the structure of the targets and was asked to predict a fold
similar to the native one out of a database of 1300 structures. In
each case the target structure was excluded from this database. Also,
the sequence homology between each target and any of the 1300 folds
was not higher than 25%. The sequence was threaded over the database
for each of 20 different parameter sets. The thread scores were
averaged and used to sort the results (model/alignments). The top
scoring results were then analyzed case by case. We looked for good
models /alignments where insertions and deletions should be in loop
regions where they could be modeled without disrupting the overall

Here we present four representative cases. Three are successful
predictions (beta spectrin, a phosphatase, a nucleoside phosphoryase),
the fourth is an unsuccessful case (NFKB P50). The quality of the
predictions and of the sequence-structure alignments was assayed by
structure-structure comparison using ProSup2.


1. Floeckner,H., Braxenthaler,M., Lackner,P.,Jaritz,M.,
Ortner,M., Sippl,M.J. Progress in fold recognition. Proteins, 23,
376-386, (1995).

2. Feng,Z.-K. & Sippl, M.J. Optimum superimposition of protein
structures, ambiguities and implications. Folding and Design, 1,
123-132, (1996).

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