BCMB 422 Computational Biology and Bioinformatics
University of Tennessee, Knoxville (teaching assistant Spring 2013)

Kraken Project

In this project, undergraduate students enrolled in the BCMB 422 Computational Biology/Bioinformatics course at the University of Tennessee, Knoxville will be given access to the Kraken Supercomputer to run high-throughput docking simulations using the VinaMPI application developed in the laboratory of Jerome Baudry with the assistance of graduate student Sally Ellingson and used in their research. Students will be exploring the use of clustering methods to extract snapshots of the protein of interest from a Molecular Dynamics simulation in order to examine unique conformational states in which the protein may exist. This is an open and exciting area of research used to discover novel pharmaceuticals that would not be discovered through traditional docking to the static crystalized protein structure. In addition to the early exposure to high-performance computing, the students will be performing novel research in computational biology. PROJECT WEBSITE