Protein Domain Boundary Predictions: A Structural Biology Perspective

Kirillova, Svetlana; Kumar, Suresh; Carugo, Oliviero

CASP is divided into several sections, ranging from prediction of conformational disorder to tertiary structure prediction. Protein domain boundary predictions began to be included in the CASP initiative in 2004. The dissection of a protein into separate structural domains is in fact not trivial at all [46, 47] . It is related to the ill-definition of what a protein domain is. An amino acid segment can be in fact consid-ered to be a structural domain if i) it is a compact ensemble of atoms/residues; ii) it is an ensemble of atoms/residues that behaves as a rigid body, in the sense that it can move relative to other protein moieties without changing its shape; iii) it is a self-folding subunit; iv) it is a polypeptide segment well conserved during molecular evolution. Given the ambiguity in any quantitative definition, the real domain boundaries were defined according to the CASP7 organizers and assessors [47] . They found a reasonable consensus definition for each investigated protein, which seems to be well suitable for a structural biology analysis.