AMS-536 Molecular Modeling of Biological Molecules

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Please see for Rizzo Group Homepage (Research and Teaching)

Instructor Dr. Robert C. Rizzo [631-632-9340, robert dot rizzo -at-]
Teaching Assistant Chris Corbo [631-632-8519, christopher dot corbo - at - stonybrook dot edu]
Teaching Assistant Brock Boysan [631-632-8519, brock dot boysan - at - stonybrook dot edu]
Course No. AMS-536 / CHE-536
Location/Time Math Tower Sinc Site, S235, Monday and Wednesday 2:30PM - 3:50PM
Office Hours Anytime or by appointment, Math Tower, Room 3-129, Dept. of Applied Math & Statistics
Acknowledgments The AMS-536 instructors would like to thank:

(1) Chemical Computing Group at for generously providing MOE software teaching licenses
(2) Firat Coskin and the entire IACS team for cluster support
(3) Pat Tonra for Mathlab support
(4) Victor Poon for other computational support

GENERAL INFORMATION: AMS-536 is designed for students who wish to gain hands-on experience modeling biological molecules at the atomic level. In conjunction with the participants' interest, Molecular Mechanics, molecular dynamics, Monte Carlo, Docking (virtual screening), or Quantum Mechanics software packages will be used. Projects will include setup, execution, and analysis. Students will work on individual projects outside of class. Course participants will give presentations relevant to the simulations being performed and a final project report will be required. Grades will be based on the quality of the talks, participation in class discussion, attendance, and the final written report. Familiarity with working in a Unix (Linux) environment is desirable.

Learning Obectives:

  • (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:
    • (i) Introduction/Background (include biological relevance)
    • (ii) Specifics of Your System
    • (iii) Computational Details (theory)
    • (iv) Computational Details (system setup)
    • (v) Results and Discussion (include a critical interpretation of your results)
    • (vi) Conclusions
    • (vii) Future
    • (viii) Acknowledgments
  • (8) Write a polished well-referenced manuscript in the format of a peer-reviewed Journal Article.

LITERATURE DISCLAIMER: Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.

PRESENTATION DISCLAIMER: Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.

Required Syllabi Statements:

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Course Schedules