2007 Spring Course Syllabus: AMS-536
Molecular Modeling of Biological Molecules
Spring 2007
2007 Spring Course Syllabus: AMS-536Molecular Modeling of Biological Molecules |
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Spring 2007 |
| Instructor: | Dr. Robert C. Rizzo [631-632-9340, rizzo@ams.sunysb.edu] |
| Course: | AMS-536 (3 Credits / 0 Audit) http://www.ams.sunysb.edu/~rizzo (go to Teaching) |
| When: | 2:20AM-3:40PM, Monday and Wednesday, Math S235
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| Office Hours: | Anytime or by appointment, Room 1-101, Dept. of Applied Math & Statistics |
| Hyperlinks accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only. |
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Final Project Guidelines and Sample Reports |
Files and Links |
| Project Guidelines | |
| Sample report | project.example.dGhyd.pdf |
Sample report |
project.example.MMPS.pdf |
Tutorials |
|
| Unix Tutorial for Beginners | http://www.ee.surrey.ac.uk/Teaching/Unix |
| Vi Text Editor Tutorial | At linux prompt type "vimtutor" (without the quotes) |
| Molecular Mechanics Tutorial | Colby College Molecular Mechanics Tutorial |
| MOE Tutorial | see Help/Tutorials and Colby College MOE Tutorial |
| AMBER8 Tutorial | AMBER8_intro.pdf |
| VMD Tutorial | http://www.ks.uiuc.edu/Research/vmd/current/docs.html#tutorials |
Software Links and Manuals |
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| AMBER | http://amber.scripps.edu/ (users manual here) |
| BOSS / MCPRO | http://zarbi.chem.yale.edu/ (users manual here) |
| DOCK | http://dock.compbio.ucsf.edu/ (users manual here) |
| MOE (Chemical Computing Group) | http://www.chemcomp.com/ (see help menu for users manual) |
| VMD (visualization software) | http://www.ks.uiuc.edu/Research/vmd/ (users manual here) |
Databases |
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| NCI (ligand database) | http://129.43.27.140/ncidb2/ |
| NIST (small molecule database) | http://webbook.nist.gov/chemistry/ |
| ZINC (ligand database) | http://blaster.docking.org/zinc/ |
Project Notes |
Links |
| MC simulation of a pure liquid | |
Presentation Date |
Particpants |
| 02/26/2007 | Ricky, Jerry |
| 02/28/2007 | Christina, Alvin |
| 03/05/2007 | Jonathan, Diana |
| 03/12/2007 | Tony, Yukiji |
| 03/14/2007 | Shyam, Vadim |
| 03/19/2007 | Rose, Freda |
| 03/21/2007 | Trent, Liang |
| 04/09/2007 | Yan, Jerry |
| 04/11/2007 | Christina, Alvin |
| 04/16/2007 | Jonathan, Diana |
| 04/18/2007 | Tony, Yukiji |
| 04/23/2007 | Shyam, Vadim |
| 04/25/2007 | Rose, Freda |
| 04/30/2007 | Trent, Liang |
| 05/02/2007 | Yan, Ricky |
| If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact Disability Support Services (631) 632-6748. 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 Disability Support Services. For procedures and information go to the following website: http://www.ehs.sunysb.edu and search Fire Safety and Evacuation and Disabilities. |