CiC: (SEA): Exploring Azure as a Platform for Interactive Protein-Protein Docking

J. Craig Venter Institute, Inc., La Jolla CA

Investigators

Abstract

This project at the J. Craig Venter Institute is developing a client-cloud application for protein-protein docking on the Azure platform. The project is designing a self-scaling computational docking server deployed in the cloud and driven by a cross-platform desktop molecular viewer. The Azure infrastructure is being explored for numerical computations with a coarse-grained parallelism. A fault-tolerant cloud component is being built to expose both programmatic and Web form interfaces. Economically optimal scaling strategies are being studied to address the fluctuating demand within each user session, using instance pooling across sessions and predictive instance deployment. A popular 3D molecular viewer PyMol is being extended with protein-protein docking operations that can be executed by the cloud component in parallel, thus making possible the interactive user-driven simulation protocols. By using a cloud platform, this project works to make the interactive protein-protein docking simulations available to any group of biologists irrespective of location, without forcing them to maintain substantial local computing resources required for such numerically intensive methodology. The docking simulations are used to uncover the details of protein-protein interactions that form the basis of functions in any living organism. The project?s code and executables are being released under an open-source license.