title: Protein domain assignment from the recurrence of locally similar structures.
abstract: Domains are basic units of protein structure and essential for exploring protein fold space and structure evolution. With the structural genomics initiative, the number of protein structures in the Protein Databank (PDB) is increasing dramatically and domain assignments need to be done automatically. Most existing structural domain assignment programs define domains using the compactness of the domains and/or the number and strength of intra-domain versus inter-domain contacts. Here we present a different approach based on the recurrence of locally similar structural pieces (LSSPs) found by one-against-all structure comparisons with a dataset of 6373 protein chains from the PDB. Residues of the query protein are clustered using LSSPs via three different procedures to define domains. This approach gives results that are comparable to several existing programs that use geometrical and other structural information explicitly. Remarkably, most of the proteins that contribute the LSSPs defining a domain do not themselves contain the domain of interest. This study shows that domains can be defined by a collection of relatively small locally similar structural pieces containing, on average, four secondary structure elements. In addition, it indicates that domains are indeed made of recurrent small structural pieces that are used to build protein structures of many different folds as suggested by recent studies.
authors.affiliation: Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: Chin-Hsien
authors.initials: CH
authors.lastname: Tai
authors.forename: Vichetra
authors.initials: V
authors.lastname: Sam
authors.forename: Jean-Francois
authors.initials: JF
authors.lastname: Gibrat
authors.forename: Jean
authors.initials: J
authors.lastname: Garnier
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Munson
authors.forename: Byungkook
authors.initials: B
authors.lastname: Lee
mesh_terms: D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins