ABodyBuilder: Automated antibody structure prediction with data-driven accuracy estimation.

ABSTRACT: Computational modeling of antibody structures plays a critical role in therapeutic antibody design. Several antibody modeling pipelines exist, but no freely available methods currently model nanobodies, provide estimates of expected model accuracy, or highlight potential issues with the antibody's experimental development. Here, we describe our automated antibody modeling pipeline, ABodyBuilder, designed to overcome these issues. The algorithm itself follows the standard 4 steps of template selection, orientation prediction, complementarity-determining region (CDR) loop modeling, and side chain prediction. ABodyBuilder then annotates the 'confidence' of the model as a probability that a component of the antibody (e.g., CDRL3 loop) will be modeled within a root-mean square deviation thresho

SUBMITTER: Leem J 

PROVIDER: S-EPMC5058620 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature