Structural information on protein-protein interactions is essential for biology. Computational methods are needed to supplement the experimental description of the interactions. Accurate modeling is based on similarity to experimentally determined ‘template’ complexes of proteins. New research in Vakser lab showed that, contrary to the common perception, modeling templates exist for almost all known protein-protein interactions (provided the components have a known structure). This suggests a new paradigm in modeling of protein interactions (protein docking): when there is a template for a monomer, there is also a template for its complex. This finding dramatically expands our ability to model protein interactions, and has far-reaching implications for the protein docking field.
The study was conducted in collaborations with Université Paris-Sud, France and University of California San Diego. The paper by Petras Kundrotas, Zhengwei Zhu, Joël Janin, and Ilya Vakser, ’Templates are available to model nearly all complexes of structurally characterized proteins’ is published in the Early Edition of Proceeding of the National Academy of Sciences USA.