Protein Domain Boundary Predictions: A Structural Biology Perspective

Kirillova, Svetlana; Kumar, Suresh; Carugo, Oliviero

It is thus easy to select a threshold value t and to predict that a protein contains only one domain if smaller than t and that it is multi-domain protein if larger than t. Table 2 shows the mcc values [see equation (1) ] observed at various threshold values and validated with a Jack-knife procedure for the proteins examined in the CASP7 experiment. It can be observed that the mcc values are obviously smaller for very small or large values of the threshold. On the contrary they are rather large (>0.6) for intermediate threshold values and the highest mcc (0.628) is observed with a threshold of 200 residues. This prediction approach is clearly very naive. It simply assumes that a protein domain has a little probability to be very large and, as a consequence, that larger proteins have a higher probability to contain two or more domains. A protein is predicted to contain a single domain if it contains less residues that t and it is predicted to contain more than one domain if it has a number of residues larger than t. Data are taken from the proteins examined in the CASP7 experiment.