PMID: 11933071Apr 5, 2002Paper

Modifications to canonical structure sequence patterns: analysis for L1 and L3

Proteins
Enrique Vargas-Madrazo, Enrique Paz-García

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.

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Citations

Jun 5, 2012·Protein Engineering, Design & Selection : PEDS·Daisuke KurodaHaruki Nakamura
Nov 7, 2014·Nature Protocols·Paolo MarcatiliAnna Tramontano
Aug 24, 2010·Journal of Molecular Biology·Jinquan LuoYiqing Feng
Nov 17, 2005·Proteins·L del Pozo YaunerB Becerril
Mar 3, 2011·Proteins·Anna ChailyanAnna Tramontano
Mar 14, 2014·Proteins·Alexey Teplyakov, Gary L Gilliland
Aug 10, 2010·Journal of Molecular Biology·Jinquan LuoJacqueline Benson
May 5, 2017·Nucleic Acids Research·Rosalba LeporeAnna Tramontano
Oct 19, 2021·Frontiers in Molecular Biosciences·Lorenzo Di RienzoRosalba Lepore

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