Abstract
Template-based methods, which utilize known protein structures, are commonly employed to model individual proteins from their sequences. Here we benchmark a template-based method, previously proposed for modeling hetero-dimeric complexes, on sets of homodimeric assemblies. The method is based on structural alignment of assembly subunits and identifies templates for the vast majority of the test targets. In many cases, the target-template pairs have sequence identity too low for reliable detection by sequence-based methods. An overall dimer geometry as well as interface residue contacts are correctly reproduced for almost half of the targets. We present analysis of the obtained models and their templates, which revealed incorrectly determined quaternary structure for a number of entries in the Protein Data Bank.
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