Difference between revisions of "2010 AMS-536 Spring"
From Rizzo_Lab
Stonybrook (talk | contribs) (→Schedule) |
Stonybrook (talk | contribs) (→Schedule) |
||
| Line 56: | Line 56: | ||
| 2010.01.25 || Group Study; '''First Day of Class''' || Organizational Meeting / Mathlab accounts | | 2010.01.25 || Group Study; '''First Day of Class''' || Organizational Meeting / Mathlab accounts | ||
|- | |- | ||
| − | | 2010.01.27 || Group Study || Visualization software #1, Misc unix skills <br> | + | | 2010.01.27 || Group Study || Visualization software #1, Misc unix skills <br> VMD, MOE, Chimera, vi, general unix cmds, shell scripting |
|- | |- | ||
| − | | 2010.02.01 || Group Study || Visualization software #2, Misc unix skills | + | | 2010.02.01 || Group Study || Visualization software #2, Misc unix skills <br> VMD, MOE, Chimera, vi, general unix cmds, shell scripting |
|- | |- | ||
| − | | 2010.02.03 || Group Study || Visualization software #3, Misc unix skills | + | | 2010.02.03 || Group Study || Visualization software #3, Misc unix skills <br> VMD, MOE, Chimera, vi, general unix cmds, shell scripting |
|- | |- | ||
| 2010.02.08 || Group Study || Tutorials: Group 1=DOCK, Group 2=AMBER | | 2010.02.08 || Group Study || Tutorials: Group 1=DOCK, Group 2=AMBER | ||
Revision as of 12:24, 25 January 2010
| 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 3:50PM - 5:10PM |
| Office Hours | Anytime or by appointment, Room 1-101, Dept. of Applied Math & Statistics |
| Teaching Assistant | Sudipto Mukherjee, 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
Note: Each participant please update the Wiki as required with the title of your talk.
| Date | Participant | Talk |
| 2010.01.25 | Group Study; First Day of Class | Organizational Meeting / Mathlab accounts |
| 2010.01.27 | Group Study | Visualization software #1, Misc unix skills VMD, MOE, Chimera, vi, general unix cmds, shell scripting |
| 2010.02.01 | Group Study | Visualization software #2, Misc unix skills VMD, MOE, Chimera, vi, general unix cmds, shell scripting |
| 2010.02.03 | Group Study | Visualization software #3, Misc unix skills VMD, MOE, Chimera, vi, general unix cmds, shell scripting |
| 2010.02.08 | Group Study | Tutorials: Group 1=DOCK, Group 2=AMBER |
| 2010.02.10 | Group Study | Tutorials: Group 1=DOCK, Group 2=AMBER |
| 2010.02.15 | Group Study | Tutorials: Group 1=DOCK, Group 2=AMBER |
| 2010.02.17 | Group Study | Tutorials: Group 1=AMBER, Group 2=DOCK / Project Discussion |
| 2010.02.22 | Group Study | Tutorials: Group 1=AMBER, Group 2=DOCK / Project Discussion |
| 2010.02.24 | Group Study | Tutorials: Group 1=AMBER, Group 2=DOCK / Project Discussion |
| 2010.03.01 | Group Study | Snow Day |
| 2010.03.03 | Group Study | Seawulf Accounts / Scripting / Project Discussion |
| 2010.03.08 | Group Study | Project Discussion / Troubleshooting |
| 2010.03.10 | Group Study | Project Discussion / Troubleshooting |
| 2010.03.15 | Steitz, Josh ; Group Study | Docking studies of Taxol and Taxol Analogs |
| 2010.03.17 | Holden, Patrick ; Group Study | An Investigation of the "Relaxed-Complex" Docking Scheme Using Acetylcholinesterease |
| 2010.03.22 | Paiva, Fabiana ; Ray, Navamita | Folding the Ten-Amino Acid Protein CLN025 ; Crossdocking Studies of Estrogen Receptors |
| 2010.03.24 | Ali, Wahida ; LeBarron, Jamie | Strand Slippage in DNA pol lambda ; MD Simulations of Membrane-bound Rhodopsin |
| 2010.03.29 | SPRING BREAK | NO CLASS |
| 2010.03.31 | SPRING BREAK | NO CLASS |
| 2010.04.05 | Steitz, Josh ; Group Study | Docking studies of Taxol and Taxol Analogs |
| 2010.04.07 | Holden, Patrick ; Group Study | An Investigation of the "Relaxed-Complex" Docking Scheme Using Acetylcholinesterease |
| 2010.04.12 | Paiva, Fabiana; Preliminary Report due | Folding the Ten-Amino Acid Protein CLN025 |
| 2010.04.14 | Ray, Navamita | Crossdocking studies of Estrogen Receptors |
| 2010.04.19 | Ali, Wahida ; Wang, Hui | Strand Slippage in DNA pol lambda ; MD simulation of hp35 |
| 2010.04.21 | LeBarron, Jamie; Dong, Xu | MD Simulations of Membrane-bound Rhodopsin ; Virtual Screening Targeting Acetylcholinesterease |
| 2010.04.26 | Guan, Xinyu ; Maier, James | Virtual Screening for Novel Inhibitors of E1 Protein in HPV ; Improvement of the ff99SB Side Chain Dihedral Parameters |
| 2010.04.28 | Guan, Xinyu ; Maier, James | Virtual Screening for Novel Inhibitors of E1 Protein in HPV ; Improvement of the ff99SB Side Chain Dihedral Parameters |
| 2010.05.03 | Guan, Xinyu ; Maier, James | Virtual Screening for Novel Inhibitors of E1 Protein in HPV ; Improvement of the ff99SB Side Chain Dihedral Parameters |
| 2010.05.05 | Group Study; Last Day of Class | Project Discussion |
| 2010.05.?? | Final written report due by 10AM, May ??, 2010. Late papers will not be accepted. See above for sample reports and detailed guidelines. | Give hard copy to Sudipto Mukherjee (Math Tower room 3-129) and email electronic copy to rizzorc@gmail.com |
