Domains constitute the structural, functional
and evolutionary units of proteins. Proteins can be built from a single
domain or an assortment of domains. In naturally occurring multi-domain
proteins, the combination almost always occurs end-to-end, i.e.,
one domain following another domain's C-terminal end. However, there are
exceptions to this general pattern, where multi-domain
proteins are formed by the insertion of a domain (insert domain)
into another domain (parent domain).
We have followed the definition of protein domains as in the SCOP
(Structural Classification of Proteins) database to identify
domain insertions in known protein structures. Although there are several
schemes for protein structure classification, SCOP is central to this
work as it is a manually curated classification of proteins of known structures
based on their structural and evolutionary relatedness.
We have considered only the major five classes (All-alpha, All-beta,
alpha/beta, alpha+beta and Small Proteins), the fold and the superfamily
level of SCOP hierarchy for identifying insertions. Apart from browsing
insertions in whole PDB, we also provide an option to browse insertions
in a pre-computed list of non-redundant PDB chains provided by PDB_Select
with a sequence identity threshold of 90%.
Please use the menu in the navigation bar and consult the FAQ page to
know more about domain insertion.
We gratefully acknowledge financial support from the Medical Research
Council and the Camrbidge Commonwealth Trust.