IMGT/3Dstructure-DB: Querying the IMGT Database for 3D Structures in Immunology and Immunoinformatics (IG or Antibodies, TR, MH, RPI, and FPIA)
- 1 June 2011
- journal article
- Published by Cold Spring Harbor Laboratory in Cold Spring Harbor Protocols
- Vol. 2011 (6) , 750-61
- https://doi.org/10.1101/pdb.prot5637
Abstract
INTRODUCTION: IMGT/3Dstructure-DB is the three-dimensional (3D) structure database of IMGT, the international ImMunoGenetics information system that is acknowledged as the global reference in immunogenetics and immunoinformatics. IMGT/3Dstructure-DB contains 3D structures of (1) antigen receptors that comprise immunoglobulins (IG) or antibodies and T cell receptors (TR), (2) major histocompatibility (MH) proteins of class I (MH1) and class II (MH2), (3) peptide/MH (pMH) complexes (pMH1, pMH2), (4) antigen receptor/antigen complexes (IG/Ag, TR/pMH), and (5) related proteins of the immune system (RPI) belonging to the immunoglobulin and MH superfamilies (IgSF and MhSF, respectively) and found in complexes with IG, TR, or MH. IMGT/3Dstructure-DB data are annotated according to the IMGT criteria, using IMGT/DomainGapAlign, and based on the IMGT-ONTOLOGY axioms and concepts. The use of IMGT/3Dstructure-DB is described here. It provides IMGT gene and allele identification (CLASSIFICATION), region and domain delimitations (DESCRIPTION), and amino acid (AA) positions according to the IMGT unique numbering (NUMEROTATION). IMGT/3Dstructure-DB provides the closest genes and alleles that are expressed in the AA sequences of the 3D structures, by aligning these sequences with the IMGT domain reference directory.Keywords
This publication has 32 references indexed in Scilit:
- IMGT, the International ImMunoGeneTics Information SystemCold Spring Harbor Protocols, 2011
- IMGT/DomainGapAlign: IMGT Standardized Analysis of Amino Acid Sequences of Variable, Constant, and Groove Domains (IG, TR, MH, IgSF, MhSF)Cold Spring Harbor Protocols, 2011
- IMGT/Collier de Perles: IMGT Standardized Representation of Domains (IG, TR, and IgSF Variable and Constant Domains, MH and MhSF Groove Domains)Cold Spring Harbor Protocols, 2011
- IMGT/JunctionAnalysis: IMGT Standardized Analysis of the V-J and V-D-J Junctions of the Rearranged Immunoglobulins (IG) and T Cell Receptors (TR)Cold Spring Harbor Protocols, 2011
- IMGT/V-QUEST: IMGT Standardized Analysis of the Immunoglobulin (IG) and T Cell Receptor (TR) Nucleotide SequencesCold Spring Harbor Protocols, 2011
- IMGT Collier de Perles for the Variable (V), Constant (C), and Groove (G) Domains of IG, TR, MH, IgSF, and MhSFCold Spring Harbor Protocols, 2011
- IMGT Unique Numbering for the Variable (V), Constant (C), and Groove (G) Domains of IG, TR, MH, IgSF, and MhSFCold Spring Harbor Protocols, 2011
- IMGT/3Dstructure-DB and IMGT/DomainGapAlign: a database and a tool for immunoglobulins or antibodies, T cell receptors, MHC, IgSF and MhcSFNucleic Acids Research, 2009
- Isolation of a human-like antibody fragment (scFv) that neutralizes ricin biological activityBMC Biotechnology, 2009
- IMGT(R), the international ImMunoGeneTics information system(R)Nucleic Acids Research, 2008