Target domain definition and classification in CASP8

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Abstract
In order to be successful CASP experiments require experimentally determined protein structures. These structures form the basis of the experiment. Structural genomics groups have provided the vast majority of these structures in recent editions of CASP. Before the structure prediction assessment can begin these target structures must be divided into structural domains for assessment purposes and each assessment unit must be assigned to one or more tertiary structure prediction categories. In CASP8 target domain boundaries were based on visual inspection of targets and their experimental data, and on superpositions of the target structures with related template structures. As in CASP7 target domains were broadly classified into two different categories: “template‐based modeling” and “free modeling.” Assessment categories were determined by structural similarity between the target domain and the nearest structural templates in the PDB and by whether or not related structural templates were used to build the models. The vast majority of the 164 assessment units in CASP8 were classified as template‐based modeling. Just 10 target domains were defined as free modeling. In addition three targets were assessed in both the free modeling and template based categories and a subset of 50 template‐based models was evaluated as part of the “high accuracy” subset. The targets submitted for CASP8 confirmed a trend that has been apparent since CASP5: targets submitted to the CASP experiments are becoming easier to predict. Proteins 2009.

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