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ProFIT prediction
results in CASP2
Domingues F., Floeckner H., Jaritz M.
and Sippl M. Center of Applied Molecular Engineering University
of Salzburg
Current methods for Protein structure prediction were tested
at the
Second Meeting on the Critical Assessment of Techniques for
Protein
Structure Prediction (CASP2).
Predictions were submitted for protein structures soon to be
released by
experimentalists. The meeting took place last December, when the
predictions were compared to the experimental models by
independent
accessors. 152 groups participated in the experiment and 947
predictions were accepted.
We participated in the Fold Recognition category, where the goal
is to
identify a fold related to a target sequence in a database of
known
structures. Also, the targets have no considerable sequence
homology
to the known folds. We used ProFIT to produce the prediction
models, and
PROSAII to evaluate them. There were 7 targets whose folds were
recognizable. We submitted predictions for 6 of these targets. We
only
submitted an additional prediction for a target that turned out
to be
a new type of fold, therefore not predictable by fold
recognition. Of
these 6 predictions, 3 of them were considered
"correct" by the
accessors, so that our model shared high structure similarity to
the
experimental one. In one case (t0031) our model was considered by
the
accessors to be the "best" accepted prediction. Besides
these
"correct" predictions, we also predicted the correct
fold type for
target t0038. The predicted model had considerable structure
homology
to the target (5 out of 9 beta strands can be superimposed to 2
A). We
failed to predict two targets. Both these targets of them were
large
multiple domain proteins.
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