Difference between revisions of "2010 AMS-536 Spring"

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| 2010.02.03 || Group Study || Visualization software #3, Misc unix skills <br> VMD, MOE, Chimera, vi, general unix cmds, shell scripting
 
| 2010.02.03 || Group Study || Visualization software #3, Misc unix skills <br> VMD, MOE, Chimera, vi, general unix cmds, shell scripting
 
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| 2010.02.08 || Group Study || Tutorials: Group 1=DOCK, Group 2=AMBER
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| 2010.02.08 || Group Study || Tutorials: Group 1=DOCK, Group 2=AMBER  
 
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| 2010.02.10 || Group Study || Tutorials: Group 1=DOCK, Group 2=AMBER
 
| 2010.02.10 || Group Study || Tutorials: Group 1=DOCK, Group 2=AMBER
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| 2010.02.15 || Group Study || Tutorials: Group 1=DOCK, Group 2=AMBER
 
| 2010.02.15 || Group Study || Tutorials: Group 1=DOCK, Group 2=AMBER
 
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| 2010.02.17 || Group Study || Tutorials: Group 1=AMBER, Group 2=DOCK / Project Discussion
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| 2010.02.17 || Group Study || Tutorials: Group 1=DOCK, Group 2=AMBER
 
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| 2010.02.22 || Group Study || Tutorials: Group 1=AMBER, Group 2=DOCK / Project Discussion
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| 2010.02.22 || Group Study || Tutorials: Group 1=AMBER, Group 2=DOCK (seawulf accounts / project discussion)
 
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| 2010.02.24 || Group Study || Tutorials: Group 1=AMBER, Group 2=DOCK / Project Discussion
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| 2010.02.24 || Group Study || Tutorials: Group 1=AMBER, Group 2=DOCK (seawulf accounts / project discussion)
 
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| 2010.03.01 || Group Study || Snow Day
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| 2010.03.01 || Group Study || Tutorials: Group 1=AMBER, Group 2=DOCK (seawulf accounts / project discussion)
 
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| 2010.03.03 || Group Study || Seawulf Accounts / Scripting / Project Discussion
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| 2010.03.03 || Group Study || Tutorials: Group 1=AMBER, Group 2=DOCK (seawulf accounts / project discussion)
 
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| 2010.03.08 || Group Study || Project Discussion / Troubleshooting  
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| 2010.03.08 || Group Study || Project Setups / Troubleshooting  
 
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| 2010.03.10 || Group Study || Project Discussion / Troubleshooting  
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| 2010.03.10 || Group Study || Project Setups / Troubleshooting  
 
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| 2010.03.15 || Steitz, Josh ; Group Study || Docking studies of Taxol and Taxol Analogs
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| 2010.03.15 || Last, First; Group Study || Talk Title; Project Setups / Troubleshooting
 
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| 2010.03.17 || Holden, Patrick ; Group Study || An Investigation of the "Relaxed-Complex" Docking Scheme Using Acetylcholinesterease
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| 2010.03.17 || Last, First; Group Study || Talk Title; Project Setups / Troubleshooting
 
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| 2010.03.22 || Paiva, Fabiana ; Ray, Navamita || Folding the Ten-Amino Acid Protein CLN025 ; Crossdocking Studies of Estrogen Receptors
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| 2010.03.22 || Last, First; Last, First|| Talk Title ; Talk Title
 
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| 2010.03.24 || Ali, Wahida ; LeBarron, Jamie || Strand Slippage in DNA pol lambda ; MD Simulations of Membrane-bound Rhodopsin
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| 2010.03.24 || Last, First; Last, First|| Talk Title ; Talk Title
 
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| 2010.03.29 || SPRING BREAK || NO CLASS
 
| 2010.03.29 || SPRING BREAK || NO CLASS
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| 2010.03.31 || SPRING BREAK || NO CLASS
 
| 2010.03.31 || SPRING BREAK || NO CLASS
 
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| 2010.04.05 || Steitz, Josh ; Group Study || Docking studies of Taxol and Taxol Analogs
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| 2010.04.05 || Last, First; Last, First|| Talk Title ; Talk Title
 
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| 2010.04.07 || Holden, Patrick ; Group Study || An Investigation of the "Relaxed-Complex" Docking Scheme Using Acetylcholinesterease
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| 2010.04.07 || Last, First; Last, First|| Talk Title ; Talk Title
 
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| 2010.04.12 || Paiva, Fabiana; '''Preliminary Report due''' || Folding the Ten-Amino Acid Protein CLN025
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| 2010.04.12 || '''Preliminary Report due''' Last, First; Last, First; || Talk Title ; Talk Title
 
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| 2010.04.14 || Ray, Navamita || Crossdocking studies of Estrogen Receptors  
 
| 2010.04.14 || Ray, Navamita || Crossdocking studies of Estrogen Receptors  

Revision as of 12:34, 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=DOCK, Group 2=AMBER
2010.02.22 Group Study Tutorials: Group 1=AMBER, Group 2=DOCK (seawulf accounts / project discussion)
2010.02.24 Group Study Tutorials: Group 1=AMBER, Group 2=DOCK (seawulf accounts / project discussion)
2010.03.01 Group Study Tutorials: Group 1=AMBER, Group 2=DOCK (seawulf accounts / project discussion)
2010.03.03 Group Study Tutorials: Group 1=AMBER, Group 2=DOCK (seawulf accounts / project discussion)
2010.03.08 Group Study Project Setups / Troubleshooting
2010.03.10 Group Study Project Setups / Troubleshooting
2010.03.15 Last, First; Group Study Talk Title; Project Setups / Troubleshooting
2010.03.17 Last, First; Group Study Talk Title; Project Setups / Troubleshooting
2010.03.22 Last, First; Last, First Talk Title ; Talk Title
2010.03.24 Last, First; Last, First Talk Title ; Talk Title
2010.03.29 SPRING BREAK NO CLASS
2010.03.31 SPRING BREAK NO CLASS
2010.04.05 Last, First; Last, First Talk Title ; Talk Title
2010.04.07 Last, First; Last, First Talk Title ; Talk Title
2010.04.12 Preliminary Report due Last, First; Last, First; Talk Title ; Talk Title
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
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