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Nucleic Acids Res. 2015 Jan;43(Database issue):D432-8. doi: 10.1093/nar/gku1106. Epub 2014 Nov 11.

PyIgClassify: a database of antibody CDR structural classifications.

Author information

1
Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA Program in Molecular and Cell Biology and Genetics, Drexel University College of Medicine, 245 N. 15th St. Philadelphia, PA 19102, USA.
2
Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA.
3
Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA Roland.Dunbrack@fccc.edu.

Abstract

Classification of the structures of the complementarity determining regions (CDRs) of antibodies is critically important for antibody structure prediction and computational design. We have previously performed a clustering of antibody CDR conformations and defined a systematic nomenclature consisting of the CDR, length and an integer starting from the largest to the smallest cluster in the data set (e.g. L1-11-1). We present PyIgClassify (for Python-based immunoglobulin classification; available at http://dunbrack2.fccc.edu/pyigclassify/), a database and web server that provides access to assignments of all CDR structures in the PDB to our classification system. The database includes assignments to the IMGT germline V regions for heavy and light chains for several species. For humanized antibodies, the assignment of the frameworks is to human germlines and the CDRs to the germlines of mice or other species sources. The database can be searched by PDB entry, cluster identifier and IMGT germline group (e.g. human IGHV1). The entire database is downloadable so that users may filter the data as needed for antibody structure analysis, prediction and design.

PMID:
25392411
PMCID:
PMC4383924
DOI:
10.1093/nar/gku1106
[Indexed for MEDLINE]
Free PMC Article

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