Protein Domain Boundary Predictions: A Structural Biology Perspective

Kirillova, Svetlana; Kumar, Suresh; Carugo, Oliviero

The definition of what is a well predicted domain is obviously arbitrary and here the following conditions were used in order to select the predictions that can be considered to be satisfactory. If the domain contains N residues and it is predicted to contain M residues, and if C is the number of residues that are found in both the real and the predicted domain, a good prediction was defined as a case in which N M < 20 (6) and C min(M , N ) > 0.95 (7) For well predicted domains, we then computed the differences between the sequence position in which the domain is predicted to begin and the sequence position in which it begins in the reality (Delta_b). Note that a negative value of Delta_b indicates that the domain is predicted to begin before the real beginning along the protein sequence. Analogously, we also computed the differences between the sequence position in which the domain is predicted to end and the sequence position in which it ends in the reality (Delta_e). A positive value of Delta_e indicates that the domain is predicted to be slightly longer, at its C-terminus, than the reality.