Difference between revisions of "2012 AMS-536 Spring"
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'''Project Approval Sheet''' | '''Project Approval Sheet''' | ||
| − | *[http:// | + | *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/projectA.student.info.doc project.student.info.doc] |
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'''Final Report Guidelines and Example Final Papers''' | '''Final Report Guidelines and Example Final Papers''' | ||
| − | *[http:// | + | *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.guidelines.pdf project.guidelines.pdf] |
| − | *[http:// | + | *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.example.dGhyd.pdf project.example.dGhyd.pdf] |
| − | *[http:// | + | *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.example.MMPS.pdf project.example.MMPS.pdf] |
<br> | <br> | ||
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| 2012.02.08 || Group Study || Cheat Sheet: [[Unix]], [[Vi]], [[C_Shell_Scripting]] | | 2012.02.08 || Group Study || Cheat Sheet: [[Unix]], [[Vi]], [[C_Shell_Scripting]] | ||
|- | |- | ||
| − | | 2012.02.13 || Group Study || Tutorials: DOCK <br> individual project discussion [http:// | + | | 2012.02.13 || Group Study || Tutorials: DOCK <br> individual project discussion [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2012.02.13.ams536.joe.docking_intro.pdf Allen, W.] |
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| 2012.02.15 || Group Study || Tutorials: DOCK <br> individual project discussion | | 2012.02.15 || Group Study || Tutorials: DOCK <br> individual project discussion | ||
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| 2012.02.27 || Group Study || Tutorials: DOCK <br> wiki editing | | 2012.02.27 || Group Study || Tutorials: DOCK <br> wiki editing | ||
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| − | | 2012.02.29 || Group Study || Tutorials: AMBER <br> individual project discussion [http:// | + | | 2012.02.29 || Group Study || Tutorials: AMBER <br> individual project discussion [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2012.02.29.ams536.lingling.amber_intro.pdf Jiang L.] |
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| 2012.03.05 || Group Study || Tutorials: AMBER <br> individual project discussion | | 2012.03.05 || Group Study || Tutorials: AMBER <br> individual project discussion | ||
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| 2012.04.04 || Spring Recess || Spring Recess | | 2012.04.04 || Spring Recess || Spring Recess | ||
|- | |- | ||
| − | | 2012.04.09 || Gan, Alfred; Qiu, Tuoling || | + | | 2012.04.09 || Gan, Alfred; Qiu, Tuoling || Elucidating the ligand-binding energetics of the GluN1 subunit ; Dynamics of HIV-1 Gp120 Binding to CD4 and Antibody 17b |
|- | |- | ||
| 2012.04.11 || '''Preliminary Report Due''' <br> Shi, Hui; Sinayev, Roman || Identification of potent inhibitors for human epidermal fatty acid binding protein ; De Novo Search | | 2012.04.11 || '''Preliminary Report Due''' <br> Shi, Hui; Sinayev, Roman || Identification of potent inhibitors for human epidermal fatty acid binding protein ; De Novo Search | ||
Latest revision as of 16:24, 5 August 2013
| Instructor | Dr. Robert C. Rizzo [631-632-8519, rizzorc@gmail.com] |
|---|---|
| Course No. | AMS-536 / CHE-536 |
| Location/Time | Math Tower, Room S235 (COMPUTER LAB next to SINC site), Mon/Wed 2:20PM - 3:40PM |
| Office Hours | Anytime or by appointment, Room 1-101, Dept. of Applied Math & Statistics |
| Teaching Assistant | Lingling Jiang, Room 3-129, 2-8519, Dept. of Applied Math & Statistics |
Project Information
Project Approval Sheet
Oral Presentation Guidlines: These meetings should be formal and your chance to tell a complete story. Talks should be presented in PPT format and be 30 minutes long. The purpose of your talks is for you to clearly and concisely present your overall progress to date including appropriate background material and interpretation of your results. Talks should be arranged in the following order:
- Introduction/Background (include biological relevance)
- Specifics of Your System
- Computational Details (theory)
- Computational Details (system setup)
- Results and Discussion (include a critical interpretation of your results)
- Conclusions
- Future
- Acknowledgments
Final Report Guidelines and Example Final Papers
Tutorials, Software Links, and Other Relevant Class Information
Schedule
- Each participant please update the Wiki as required with the title of your talk.
- Please note that a doctors excuse will be required if you miss your scheduled oral presentation date because of illness.
| Date | Participant | Talk |
| 2012.01.23 | First Day of Class and Organizational Meeting Group Study |
Mathlab account setups, Unix and vi tutorials (1) http://www.ee.surrey.ac.uk/Teaching/Unix (2) At Linux command prompt type "vimtutor" (without the quotes) to start a built in tutorial for the text editor program called vi |
| 2012.01.25 | Group Study | Continue Mathlab account setups, Unix and vi tutorials (1) http://www.ee.surrey.ac.uk/Teaching/Unix (2) At Linux command prompt type "vimtutor" (without the quotes) to start a built in tutorial for the text editor program called vi |
| 2012.01.30 | Group Study | Visualization/analysis software, VMD, MOE, Chimera, Seawulf account setups, environments, shell scripting, misc unix |
| 2012.02.01 | Group Study | Visualization/analysis software, VMD, MOE, Chimera, Seawulf account setups, environments, shell scripting, misc unix |
| 2012.02.06 | Group Study | Visualization/analysis software, VMD, MOE, Chimera, Seawulf account setups, environments, shell scripting, misc unix |
| 2012.02.08 | Group Study | Cheat Sheet: Unix, Vi, C_Shell_Scripting |
| 2012.02.13 | Group Study | Tutorials: DOCK individual project discussion Allen, W. |
| 2012.02.15 | Group Study | Tutorials: DOCK individual project discussion |
| 2012.02.20 | Group Study | Tutorials: DOCK individual project discussion |
| 2012.02.22 | Group Study | Tutorials: DOCK individual project discussion |
| 2012.02.27 | Group Study | Tutorials: DOCK wiki editing |
| 2012.02.29 | Group Study | Tutorials: AMBER individual project discussion Jiang L. |
| 2012.03.05 | Group Study | Tutorials: AMBER individual project discussion |
| 2012.03.07 | Group Study | Tutorials: AMBER individual project discussion |
| 2012.03.12 | Group Study | Tutorials: AMBER individual project discussion |
| 2012.03.14 | Group Study | Tutorials: AMBER wiki editing |
| 2012.03.19 | Group Study | Project Setups / Troubleshooting |
| 2012.03.21 | Group Study | Project Setups / Troubleshooting |
| 2012.03.26 | Choi, WooSuk; Guja, Kip | Computational Identification of Specific Interactions between Mitochondrial Transcription Factor A and LSP ; Computational analysis of ligand binding by mitochondrial transcription factor B1 |
| 2012.03.28 | Klaritch, Barbara; Zhou, Yuchen | Conformational Study of Erythromycin: Ensemble Differences between Unbound Molecules and Molecules Bound to the 50S Ribosomal Subunit of Thermus Thermophilus; Molecular property volume overlap as a measure of molecular similarity |
| 2012.04.02 | Spring Recess | Spring Recess |
| 2012.04.04 | Spring Recess | Spring Recess |
| 2012.04.09 | Gan, Alfred; Qiu, Tuoling | Elucidating the ligand-binding energetics of the GluN1 subunit ; Dynamics of HIV-1 Gp120 Binding to CD4 and Antibody 17b |
| 2012.04.11 | Preliminary Report Due Shi, Hui; Sinayev, Roman |
Identification of potent inhibitors for human epidermal fatty acid binding protein ; De Novo Search |
| 2012.04.16 | Wei, Longfei; Xia, Yunting | Discovery of Potential Brain Fatty Acid-binding Protein (B-FABP) Inhibitors as Drug Candidates by Virtual Screening ; Conformational Determination of a Glycopeptide Molecule |
| 2012.04.18 | Choi, WooSuk; Guja, Kip | Computational Identification of Specific Interactions between Mitochondrial Transcription Factor A and LSP ; Computational analysis of ligand binding by mitochondrial transcription factor B1 |
| 2012.04.23 | Klaritch, Barbara; Zhou, Yuchen | Conformational Study of Erythromycin: Ensemble Differences between Unbound Molecules and Molecules Bound to the 50S Ribosomal Subunit of Thermus Thermophilus ; Molecular property volume overlap as a measure of molecular similarity |
| 2012.04.25 | Gan, Alfred; Qiu, Tuoling | Elucidating the ligand-binding energetics of the GluN1 subunit ; Dynamics of HIV-1 Gp120 Binding to CD4 and Antibody 17b |
| 2012.04.30 | Shi, Hui; Sinayev, Roman | Identification of potent inhibitors for human epidermal fatty acid binding protein ; De Novo Search |
| 2012.05.02 | Last Day of Class Wei, Longfei; Xia, Yunting |
Discovery of Potential Brain Fatty Acid-binding Protein (B-FABP) Inhibitors as Drug Candidates by Virtual Screening ; Conformational Determination of a Glycopeptide Molecule |
| 2012.05.09 | Final written report due by 5PM today. Late papers will not be accepted. See above for sample reports and detailed guidelines. | Give hard copy to Lingling Jiang (Math Tower room 3-129) and email electronic copy to rizzorc@gmail.com |
