Difference between revisions of "2010 AMS-536 Spring"

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| '''Talk'''
 
| '''Talk'''
 
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| 2009.01.26 || Group Study; '''First Day of Class''' || Organizational Meeting / Mathlab accounts
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| 2010.01.25 || Group Study; '''First Day of Class''' || Organizational Meeting / Mathlab accounts
 
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| 2009.01.28 || Group Study || Visualization software demo #1, Misc unix skills  
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| 2010.01.27 || Group Study || Visualization software demo #1, Misc unix skills  
 
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| 2009.02.02 || Group Study || Visualization software demo #2, Misc unix skills  
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| 2010.02.01 || Group Study || Visualization software demo #2, Misc unix skills  
 
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|-
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| 2009.02.04 || Group Study || Visualization software demo #3, Misc unix skills
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| 2010.02.03 || Group Study || Visualization software demo #3, Misc unix skills
 
|-
 
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| 2009.02.09 || 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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| 2009.02.11 || 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
 
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| 2009.02.16 || 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
 
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| 2009.02.18 || Group Study || Tutorials: Group 1=AMBER, Group 2=DOCK / Project Discussion
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| 2010.02.17 || Group Study || Tutorials: Group 1=AMBER, Group 2=DOCK / Project Discussion
 
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| 2009.02.23 || 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 / Project Discussion
 
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| 2009.02.25 || 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 / Project Discussion
 
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| 2009.03.02 || Group Study || Snow Day
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| 2010.03.01 || Group Study || Snow Day
 
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| 2009.03.04 || Group Study || Seawulf Accounts / Scripting / Project Discussion
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| 2010.03.03 || Group Study || Seawulf Accounts / Scripting / Project Discussion
 
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| 2009.03.09 || Group Study || Project Discussion / Troubleshooting  
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| 2010.03.08 || Group Study || Project Discussion / Troubleshooting  
 
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| 2009.03.11 || Group Study || Project Discussion / Troubleshooting  
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| 2010.03.10 || Group Study || Project Discussion / Troubleshooting  
 
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| 2009.03.16 || Steitz, Josh ; Group Study || Docking studies of Taxol and Taxol Analogs
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| 2010.03.15 || Steitz, Josh ; Group Study || Docking studies of Taxol and Taxol Analogs
 
|-
 
|-
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| 2009.03.18 || Holden, Patrick ; Group Study || An Investigation of the "Relaxed-Complex" Docking Scheme Using Acetylcholinesterease
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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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| 2009.03.23 || Paiva, Fabiana ; Ray, Navamita || Folding the Ten-Amino Acid Protein CLN025 ; Crossdocking Studies of Estrogen Receptors
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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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| 2009.03.25 || Ali, Wahida ; LeBarron, Jamie || Strand Slippage in DNA pol lambda ; MD Simulations of Membrane-bound Rhodopsin
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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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| 2009.03.30 || Wang, Hui; Dong, Xu || MD simulation of hp35 ; Virtual Screening Targeting Acetylcholinesterease
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| 2010.03.29 || SPRING BREAK || NO CLASS
 
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| 2009.04.01 || Guan, Xinyu ; Maier, James || Virtual Screening for Novel Inhibitors of E1 Protein in HPV ; Improvement of the ff99SB Side Chain Dihedral Parameters
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| 2010.03.31 || SPRING BREAK || NO CLASS
 
|-
 
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| 2009.04.06 || 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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| 2009.04.08 || SPRING BREAK || NO CLASS
+
| 2010.04.07 || Holden, Patrick ; Group Study || An Investigation of the "Relaxed-Complex" Docking Scheme Using Acetylcholinesterease
 
|-
 
|-
−
| 2009.04.13 || Steitz, Josh ; Group Study || Docking studies of Taxol and Taxol Analogs
+
| 2010.04.12 || Paiva, Fabiana; '''Preliminary Report due''' || Folding the Ten-Amino Acid Protein CLN025
 
|-
 
|-
−
| 2009.04.15 || Holden, Patrick ; Group Study || An Investigation of the "Relaxed-Complex" Docking Scheme Using Acetylcholinesterease
+
| 2010.04.14 || Ray, Navamita || Crossdocking studies of Estrogen Receptors
 
|-
 
|-
−
| 2009.04.20 || Paiva, Fabiana; '''Preliminary Report due''' || Folding the Ten-Amino Acid Protein CLN025
+
| 2010.04.19 || Ali, Wahida ; Wang, Hui || Strand Slippage in DNA pol lambda ; MD simulation of hp35
 
|-
 
|-
−
| 2009.04.22 || Ray, Navamita || Crossdocking studies of Estrogen Receptors
+
| 2010.04.21 || LeBarron, Jamie; Dong, Xu || MD Simulations of Membrane-bound Rhodopsin ; Virtual Screening Targeting Acetylcholinesterease
 
|-
 
|-
−
| 2009.04.27 || Ali, Wahida ; Wang, Hui || Strand Slippage in DNA pol lambda ; MD simulation of hp35
+
| 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
 
|-
 
|-
−
| 2009.04.29 || LeBarron, Jamie; Dong, Xu || MD Simulations of Membrane-bound Rhodopsin ; Virtual Screening Targeting Acetylcholinesterease
+
| 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
 
|-
 
|-
−
| 2009.05.04 || 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  
 
|-
 
|-
−
| 2009.05.06 || Group Study; '''Last Day of Class''' || Project Discussion  
+
| 2010.05.05 || Group Study; '''Last Day of Class''' || Project Discussion  
 
|-
 
|-
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| 2009.05.12 || '''Final written report due by 10AM, Tues May 12, 2009. 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'''
+
| 2010.05.12 || '''Final written report due by 10AM, Tues May 12, 2009. 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'''
 
|-
 
|-
 
|}
 
|}

Revision as of 12:11, 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 demo #1, Misc unix skills
2010.02.01 Group Study Visualization software demo #2, Misc unix skills
2010.02.03 Group Study Visualization software demo #3, Misc unix skills
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
2010.05.12 Final written report due by 10AM, Tues May 12, 2009. 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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