Second antibody modeling assessment (AMA‐II)

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<jats:title>ABSTRACT</jats:title><jats:p>To assess the state of the art in antibody 3D modeling, 11 unpublished high‐resolution x‐ray Fab crystal structures from diverse species and covering a wide range of antigen‐binding site conformations were used as a benchmark to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 <jats:italic>et al</jats:italic>., 2011;79:3050). Proteins 2014; 82:1553–1562. © 2014 Wiley Periodicals, Inc.</jats:p>

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