Automated Aufbau of antibody structures from given sequences using Macromoltek's SmrtMolAntibody

This study was a part of the second antibody modeling assessment. The assessment is a blind study of the performance of multiple software programs used for antibody homology modeling. In the study, research groups were given sequences for 11 antibodies and asked to predict their corresponding structures. The results were measured using root-mean-square deviation (rmsd) between the submitted models and X-ray crystal structures. In 10 of 11 cases, the results using SmrtMolAntibody show good agreement between the submitted models and X-ray crystal structures. In the first stage, the average rmsd was 1.4 angstrom. Average rmsd values for the framework was 1.2 angstrom and for the H3 loop was 3.0 angstrom. In stage two, there was a slight improvement with an rmsd for the H3 loop of 2.9 angstrom. (C) 2014 Wiley Periodicals, Inc.