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Modifications to canonical structure sequence patterns: Analysis for L1 and L3
Author(s) -
VargasMadrazo Enrique,
PazGarcía Enrique
Publication year - 2002
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.10187
Subject(s) - sequence (biology) , non canonical , computational biology , computer science , biology , genetics , microbiology and biotechnology
Abstract The conformation of five of the six hypervariable loops that form the antigen‐binding site of antibodies is limited to a small set of structures designated as canonical structures. The canonical structure model has been constituted as a fundamental tool for the modeling of antibodies. The detailed study of tens of crystallographic structures of antibodies has shown the validity of this model in the great majority of cases. The robustness of the forecast capacity of this model depends fundamentally on the precision with which the sequence patterns that characterize each canonical structure form can be defined. Nevertheless, due to the enormous quantity of structural information about antibodies generated during the last decade, it is difficult to avoid mistakes or confusion in the model. In the present work, we propose some corrections to the model for loops L1 and L3 that permit defining sequence patterns that avoid confusion and make better forecasting of the canonical structure model possible. Proteins 2002;47:250–254. © 2002 Wiley‐Liss, Inc.