Access Methods

Although there are several schemes for protein structure classification for investigating protein sequences and structures, SCOP is important as it is a manually curated classification of proteins of know structures from the protein data Bank based on their structural and evolutionary relatedness. In SCOP, a protein domain is considered as an unit of evolution if it occurs independently or in combination with other domains on the basis of evidence from proteins of known structure. SCOP has a hierarchical classification scheme with the principal levels being family, superfamily, fold and class. Proteins clustered together into families are clearly evolutionarily related, usually detectable at sequence level. Proteins brought together into superfamilies although have low sequence identity, their structural and functional features suggest a common evolutionary origin. Superfamilies with similar topology, but without evidence for evolutionary relatedness are grouped under a fold. Folds are then classified into classes based on the secondary structure elements present.

      We have considered only the first five classes (All-alpha, All-beta, alpha/beta, alpha+beta and Small proteins), the fold and the superfamily level of SCOP hierarchy for determining insertions. We excluded mono-domain proteins and considered chains which have at least two domains in them. In multi-domain proteins, while it is usual to have two domains linked in a linear fashion, i.e., the C-terminus of the first domain covalently linked to the N-terminus of the second domain, we looked for domains which are interrupted in the middle by the insertion of another domain. Thus, the second domain (insert) begins and ends inside the first domain (parent domain). The domains involved in insertions can come from the same or different SCOP superfamily.