UT/ORNL Center for Molecular Biophysics

BCMB422 Computational Biology / Bioinformatics

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.

Workshop Outline



Week 1 (April 2 & 4)

  • Lecture on ensemble docking
  • Login to accounts
Download Instructions
Download Lecture

  • Run a sample job with all files prepared
  • Analyze results
Download Instructions
Basic Commands
Check Job
File Transfer

Week 2 (April 16 & 18)

In class project:

  • Students will repeat process but prepare files themselves and change at least one aspect (i.e. different clustering, different threshold, different box center, different box dimensions)
  • Class time will be used for students to work independently and ask questions
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Week 3 (April 23 & 25)

Students get 5 minutes each to present their results (due to time constraints and difficulty of the project, this time will be dedicated to more in class work time)


Contact Information

Jerome Baudry
jbaudry at utk dot edu

Sally R. Ellingson
sellings at utk dot edu