MoFvAb: Modeling the Fv region of antibodies

Alexander Bujotzek, Angelika Fuchs, Changtao Qu, Jö Org Benz, Stefan Klostermann, Iris Antes, Guy Georges

Research output: Contribution to journalArticlepeer-review

20 Scopus citations

Abstract

Knowledge of the 3-dimensional structure of the antigen-binding region of antibodies enables numerous useful applications regarding the design and development of antibody-based drugs. We present a knowledge-based antibody structure prediction methodology that incorporates concepts that have arisen from an applied antibody engineering environment. The protocol exploits the rich and continuously growing supply of experimentally derived antibody structures available to predict CDR loop conformations and the packing of heavy and light chain quickly and without user intervention. The homology models are refined by a novel antibody-specific approach to adapt and rearrange sidechains based on their chemical environment. The method achieves very competitive all-atom root mean square deviation values in the order of 1.5 Å on different evaluation datasets consisting of both known and previously unpublished antibody crystal structures.

Original languageEnglish
Pages (from-to)838-852
Number of pages15
JournalmAbs
Volume7
Issue number5
DOIs
StatePublished - 2015

Keywords

  • Amino acid sidechain conformation
  • Antibody structure
  • Homology modeling
  • Macromolecular modeling
  • Protein domain orientation
  • Protein engineering
  • Protein structure prediction

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