Protein-protein interactions are central for cellular processes. Physical characterization of these interactions is essential for understanding biomolecular mechanisms and for applications in biology and medicine. Experimentally determined protein structures and their complexes account only for a fraction of known protein interactions. Thus, structural modeling of these interactions (docking), in most cases, has to rely on models of the individual proteins. The docking approaches have to be tested on carefully curated, comprehensive sets of protein models with controlled levels of structural inaccuracy. Benchmark sets of such protein models were developed. For each protein, a comprehensive array of models was generated. The highest accuracy of the predicted complexes, which can be achieved using the structures in the set, was estimated. Comprehensive benchmarking on the set showed that the existing docking approaches reliably model protein-protein complexes at different levels of proteins structural accuracy. Conformational properties of protein interfaces were investigated to explore the opportunities to modulate protein interactions. Refinement procedures were developed, to increase the structural accuracy of modeling.

Modeling interactions of predicted proteins

251st National Meeting (2016)

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