AMS-536 Molecular Modeling of Biological Molecules

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Please see for Rizzo Group Homepage (Research and Teaching)

Instructor Dr. William J. Allen [631-632-8519,]

Dr. Robert C. Rizzo [631-632-8519,]

Course No. AMS-536 / CHE-536
Location/Time Math Tower, Room S235 (COMPUTER LAB next to SINC site), Mon/Wed 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) Yan Yu and the Seawulf team for cluster support
(3) Pat Tonra for Mathlab 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. Familiarity with working in a Unix (Linux) environment is desirable.

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: The University Senate has authorized that the following required statements appear in all teaching syllabi on the Stony Brook Campus. This information is also located on the Provost’s website:

Americans with Disabilities Act: If you have a physical, psychological, medical or learning disability that may impact your course work, please contact Disability Support Services, ECC(Educational Communications Center) Building, Room 128, (631)632-6748. They will determine with you what accommodations, if any, are necessary and appropriate. All information and documentation is confidential.

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Course Schedules