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AMS 536, Molecular Modeling of Biological Molecules
This course is designed for students who wish to gain hands on experience modeling biological molecules at the atomic level. In conjunction with individual interests, Molecular Mechanics, Molecular dynamics, Monte Carlo, Docking (virtual screening), or Quantum Mechanics software packages can be used to study relevant biological systems(s). Projects will include setup, execution, and analysis. Course participants will give literature presentations relevant to the simulations being performed and a final project report will be required. Familiarity with Unix (Linux) is desirable.
PrerequisiteAMS 535 or permission of the instructor
3 credits, ABCF grading 

Text: There are no textbooks required for this course. See course website notes at

AMS 536 Instructor page

Fall Semester

Learning Outcomes:

1) Gain hands-on experience modeling biological molecules at the atomic level.

2) Learn to navigate linx/unix operating system.

3) Learn shell scripting and text-based editing (vim program).

4) Learn to use a linux-based computing cluster that has a queuing system.

5) Learn to use visualization software (Chimera, MOE, and VMD programs).

6) Setup, execute, and analyze docking (DOCK) and molecular dynamics (AMBER) tutorials.

7) Give oral presentations on individual research projects which includes:
      * Introduction/Background (include biological relevance);
      * Specifics of Your System;
      * Computational Details (theory);
      * Computational Details (system setup);
      * Results and Discussion (include a critical interpretation of your results);
      * Conclusions;
      * Future;
      * Acknowledgments.

8) Write a polished well-referenced manuscript in the format of a peer-reviewed Journal Article.

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