Distinguished Speaker Series: Large‐scale Modeling of Protein Interactions

Abstract:

Protein docking is one of the focal points of activity in computational biology. I will present new results that contribute to better understanding of fundamental properties of protein interactions, and to the development of powerful tools for their modeling. Structure‐function relationships were systematically studied by correlating protein function with the global and local similarity of the protein structures. The docking procedure was developed further to make it more adequate to the challenges of the interactome modeling. The development made use of the rapidly growing body of experimentally determined structures. The approaches were tested on large benchmark sets of protein models, and in the blind CAPRI assessment. Systematic comparison of full and interface structural alignments in protein docking showed similar success rates. The full alignment performed better for proteins with different binding sites corresponding to different functions, whereas the interface alignment showed better results for multidomain proteins. Free docking has a built‐in penalty for clashes, due to the surface complementarity paradigm. The resultsshowed that the quality of unrefined models in comparative docking is similar to that in the free docking, suggesting the use of the same structural refinement. New approaches were put forward with the ultimate goal of structural modeling of a cell, as a new emerging frontier in computational biology. 

Host:

Prof. Nir Ben‐Tal, Email: bental@tauex.tau.ac.il, Life Sciences Faculty, TAU