IMGT/Collier de Perles: IMGT Standardized Representation of Domains (IG, TR, and IgSF Variable and Constant Domains, MH and MhSF Groove Domains)

Abstract

INTRODUCTIONIMGT/Collier de Perles is the IMGT online tool that allows one to draw standardized IMGT two-dimensional (2D) graphical representations of protein domains, or IMGT Colliers de Perles, starting from the user’s own domain amino acid (AA) sequences. The use of this tool is described here. IMGT Colliers de Perles can be drawn for three domain types: the variable (V) domain and constant (C) domain of the immunoglobulin (IG) and T cell receptor (TR) and other members of the immunoglobulin superfamily (IgSF), and the groove (G) domain of the major histocompatibility (MH) and other members of the MH superfamily (MhSF). Sequences have to be gapped according to the IMGT unique numbering, using, for example, IMGT/DomainGapAlign. Resulting IMGT Colliers de Perles allow one to quickly visualize amino acids, which are important for the three-dimensional (3D) structural configuration, and to delimit the standardized framework regions (FR-IMGT) and complementarity determining regions (CDR-IMGT) of the IG and TR V-DOMAIN. The length of the strands, loops, and turns and, for the G type, the length of the helix represented in IMGT Colliers de Perles become crucial information in the domain characterization.