AMS-536 Molecular Modeling of Biological Molecules
Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage (Research and Teaching)
|Supervisor||Dr. Robert C. Rizzo [631-632-9340, robert dot rizzo -at- stonybrook.edu]|
|Instructor||Dr. Guilherme Duarte Ramos Matos [631-632-8519, guilherme dot duarteramosmatos -at- stonybrook dot edu]|
|Teaching Assistant||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
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.
- (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: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php
Student Accessibility Support Center Statement: If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at email@example.com. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential.
Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.
- To access mental health services, call Counseling and Psychological Services at 631-632-6720; Counselors are available to speak with 24/7.
- For updated information on the Academic Success and Tutoring Center please check www.stonybrook.edu/tutoring for the most up-to-date information.
- For IT Support: Students can visit the Keep Learning website at https://sites.google.com/stonybrook.edu/keeplearning for information on the tools you need for alternative and online learning. Need help? Report technical issues at https://it.stonybrook.edu/services/itsm or call 631-632-2358.
- For information on Library services and resources please visit the Continuity of Library Operations guide.
Faculty Technical Support Statement:
- Faculty needing to access information on using instructional technology for remote teaching should visit https://it.stonybrook.edu/keep-teaching
- If you experience problems using technology, please submit a service ticket at: https://it.stonybrook.edu/services/itsm
- CELT will provide remote support by Zoom at: https://stonybrook.zoom.us/j/478142498 or by email at: firstname.lastname@example.org
Academic Integrity Statement: 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/commcms/academic_integrity/index.html
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.
- 2005 AMS-536 Spring
- 2006 AMS-536 Spring
- 2007 AMS-536 Spring
- 2008 AMS-536 Spring
- 2009 AMS-536 Spring
- 2010 AMS-536 Spring
- 2011 AMS-536 Spring
- 2012 AMS-536 Spring
- 2013 AMS-536 Spring
- 2014 AMS-536 Spring
- 2015 AMS-536 Spring
- 2016 AMS-536 Spring
- 2017 AMS-536 Spring
- 2018 AMS-536 Spring
- 2019 AMS-536 Spring
- 2020 AMS-536 Spring
- 2021 AMS-536 Spring