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MILES trainees developed a course on the applications of molecular modeling


MILES IGERT trainees Joe Allen and Justin Lemkul under the guidance of their advisor Dr. David Bevan from the Biochemistry Department developed and designed the Applications for Molecular Modeling course taught for the first time in the fall 2009. The Molecular Modeling class (BCHM 5984) is designed for graduate students and senior-level undergraduate students who have a background in biological sciences and/or computational biology. The course focuses on practical and basic theoretical aspects of molecular modeling, such that the student can apply the techniques in their own research.

Emphasis is placed on understanding current literature and applying techniques to real-world problems. The purpose of the course emanates from the increasing accessibility of high-powered computing and molecular modeling software, computational techniques are becoming more widely used in biological research. This course is designed to teach students with an interest in molecular modeling the basic theories and common techniques that may be readily applied to their own research. Discussions are focused on protein modeling, but many of the techniques are easily applied to other molecules and systems of interest. Although a brief review of basic protein biochemistry will be provided, students are expected to have prior knowledge of protein structure and function. The course objectives are: 1) Describe the basic theoretical aspects of molecular modeling techniques. 2) Evaluate the successes and limitations of molecular modeling. 3) Analyze the results of molecular modeling calculations. 4) Evaluate and discuss current literature related to molecular modeling. 5) Apply molecular modeling techniques to ongoing research.

Address Goals

MILES Professor David Bevan and MILES trainees Joe Allen and Justin Lemkul are using cutting-edge computer simulations to aid in developing therapeutics for neurological disorders including Parkinson’s and Alzheimer’s diseases. Using molecular dynamics (MD) simulations to study the interactions between proteins, enzymes, and small proteins had provided valuable information related to drug and therapeutic development. Justin and Joe developed the class to share their knowledge of MD simulations to undergraduate and other MILES graduate students interested in learning this technique. This course helps to bridge the gap between computer simulations and laboratory benchtop research, ultimately increasing scientific understanding and cross-disciplinary communications among VT MILES students and faculty.