title: Second antibody modeling assessment (AMA-II).
abstract: To assess the state of the art in antibody 3D modeling, 11 unpublished high-resolution x-ray Fab crystal structures from diverse species and covering a wide range of antigen-binding site conformations were used as a benchmark to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).
authors.affiliation: CTI Boston, Pfizer Inc., 3 Blackfan Circle, 18 Floor, Boston, MA, 02115.
authors.forename: Juan C
authors.initials: JC
authors.lastname: Almagro
authors.forename: Alexey
authors.initials: A
authors.lastname: Teplyakov
authors.forename: Jinquan
authors.initials: J
authors.lastname: Luo
authors.forename: Raymond W
authors.initials: RW
authors.lastname: Sweet
authors.forename: Sreekumar
authors.initials: S
authors.lastname: Kodangattil
authors.forename: Francisco
authors.initials: F
authors.lastname: Hernandez-Guzman
authors.forename: Gary L
authors.initials: GL
authors.lastname: Gilliland
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001666:Binding Sites, Antibody; D018360:Crystallography, X-Ray; D006801:Humans; D007140:Immunoglobulin Fab Fragments / Q000737:chemistry*; D051379:Mice; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011817:Rabbits
chemical_list: D007140:Immunoglobulin Fab Fragments
keywords: antigen-binding site; canonical structures; homology modeling; immunoglobulin; x-ray structure