AMS-536 Molecular Modeling of Biological Molecules

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Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage (Research and Teaching)


Instructor Dr. Robert C. Rizzo [631-632-9340, robert.rizzo@stonybrook.edu]
Teaching Assistant Guilherme Matos [631-632-8519, Guilherme.duarteramosmatos [at] stonybrook [dot] edu] and Steve Telehany [631-632-8519, stephen dot telehany - at - stonybrook dot edu]
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 http://www.chemcomp.com for generously providing MOE software teaching licenses
(2) Firat Coskin and the entire IACS 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. 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: 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: http://www.stonybrook.edu/commcms/provost/policies.shtml


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. https://web.stonybrook.edu/newfaculty/StudentResources/Pages/DisabilitySupportServices.aspx.


Academic Integrity: Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/uaa/academicjudiciary/


Critical Incident Management: Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of University Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Faculty in the HSC Schools and the School of Medicine are required to follow their school-specific procedures. Further information about most academic matters can be found in the Undergraduate Bulletin, the Undergraduate Class Schedule, and the Faculty-Employee Handbook.

Course Schedules

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