Abstract:

The interplay between proteins, DNA, RNA and other compounds (like small molecules etc.) constitutes the interactome of an organism, which defines its behavior and characteristics. Methods to make working models (atomic systems-based) of the entire interactome of organisms will lead to better understanding of the cellular machinery to improve human health and quality of life. In this tutorial, we will first go over abstract concepts to illustrate our general modeling paradigm in the context of protein structure, function and protein interaction. We will provide specific details that relate the abstract concepts to concrete algorithms and results. Specifically, we will be talking about our work on the computational analysis of novel drug opportunities (CANDO) based on performing a shotgun in virtuale screen of all known drugs and drug-like compounds against all known and modelable protein structures to do proteome based drug discovery to find new uses for existing drugs and drug-like compounds, with a focus on underserved diseases or those indications where treatment options have been exhausted. Modeling protein complexes using the interolog method is a straightforward application of homology modeling. Modeling protein-nucleic acid and protein-compound interactions is made possible by the all atom potentials and the evolutionary interaction network based docking with dynamics methods we have developed. Integrating all this information will create all atom models of entire biological systems. We have developed infrastructure to store and manage all the data and software produced by our group, almost all of which are freely available. We will present the current challenges and limitations of our methods and future directions. This tutorial will be beneficial for researchers beginning to explore the areas of atomic level systems biology.

Speaker: Gaurav Chopra, Department of Microbiology, University of Washington, Seattle, WA, USA and Department
of Structural Biology, Stanford University, CA, USA

Requirements: Participants should have their laptops that could connect to the internet

Participant Number: 50 persons