Second antibody modeling assessment (AMA-II)

Proteins. 2014 Aug;82(8):1553-62. doi: 10.1002/prot.24567. Epub 2014 Apr 26.


To assess the state of the art in antibody 3D modeling, 11 unpublished high-resolution x-ray Fab crystal structures from diverse species and covering a wide range of antigen-binding site conformations were used as a benchmark to compare Fv models generated by seven structure prediction methodologies. The participants included: Accerlys Inc, Chemical Computer Group (CCG), Schrodinger, Jeff Gray's lab at John Hopkins University, Macromoltek, Astellas Pharma/Osaka University and Prediction of ImmunoGlobulin Structure (PIGS). The sequences of benchmark structures were submitted to the modelers and PIGS, and a set of models were generated for each structure. We provide here an overview of the organization, participants and main results of this second antibody modeling assessment (AMA-II). Also, we compare the results with the first antibody assessment published in this journal (Almagro et al., 2011;79:3050).

Keywords: antigen-binding site; canonical structures; homology modeling; immunoglobulin; x-ray structure.

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Binding Sites, Antibody
  • Crystallography, X-Ray
  • Humans
  • Immunoglobulin Fab Fragments / chemistry*
  • Mice
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Conformation
  • Rabbits


  • Immunoglobulin Fab Fragments