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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. ## Back to the list of abstracts