Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations - September 10-14, 2014, Istanbul, Turkey

Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery Session VII Abstracts

Protein-Protein Docking and Design Zhiping Weng , Thom Vreven, and Brian Pierce University of Massachusetts Medical School, Worcester, MA, USA

Protein-protein interaction is highly important for many cellular processes. We have built computational algorithms and benchmarks to predict the 3D structures of protein-protein complexes (protein-protein docking). I will present our recent work on both scoring function and search algorithm to improve protein-protein docking accuracy. In addition, we have built computational algorithms and an affinity benchmark for designing proteins to achieve stronger and more specific binding to another protein (protein design). We have thus far focused on designing T cell receptors and I will report on our recent progress.

Structural Networks of Signaling Pathways on Proteome Scale: Challenges and Opportunities Attila Gursoy . Koc University, Istanbul, Turkey. Recent advances in high-throughput techniques have resulted in large amount of data on protein structure and protein-protein interactions. Networks of protein–protein interactions provide valuable information in understanding of cellular functions and biological processes. However, these networks lack structural (3D) details of most interactions, and these structural details are the key components usually for understanding the function of proteins. Augmenting protein interaction networks with structural data at proteome scale (3D interactome) is a challenging task, at the same time, extremely important because it allows prediction of protein function, helps drug discovery and takes steps toward genome-wide structural systems biology. In this talk, the challenges in building such networks will be discussed and a computationally feasible way towards building them using protein interfaces will be presented. Structural protein interaction networks can indicate which binding partners can interact simultaneously and which are competitive, how signals coming from different upstream pathways merge and propagate downstream, how multi-subunit signaling complexes form. They can help drug discovery along the line of emerging network medicine paradigm, and can help forecasting potentially harmful drug side effects.

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