Difference between revisions of "2010 AMS-536 Spring"

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| '''Office Hours''' || Anytime or by appointment, Room 1-101, Dept. of Applied Math & Statistics
 
| '''Office Hours''' || Anytime or by appointment, Room 1-101, Dept. of Applied Math & Statistics
 
|-
 
|-
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| '''Teaching Assistant''' || Sudipto Mukherjee, Room 3-129, Dept. of Applied Math & Statistics
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| '''Teaching Assistant''' || Sudipto Mukherjee, Room 3-129, 2-8519, Dept. of Applied Math & Statistics
 
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|-
 
|}
 
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'''Project Approval Sheet'''
 
'''Project Approval Sheet'''
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*[http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.student.info.doc project.student.info.doc]
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*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.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'''
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*[http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.guidelines.pdf project.guidelines.pdf]
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*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.guidelines.pdf project.guidelines.pdf]
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*[http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.example.dGhyd.pdf project.example.dGhyd.pdf]
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*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.example.dGhyd.pdf project.example.dGhyd.pdf]
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*[http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.example.MMPS.pdf project.example.MMPS.pdf]
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*[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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| '''Talk'''
 
| '''Talk'''
 
|-
 
|-
−
| 2009.01.26 || Group Study; '''First Day of Class''' || Organizational Meeting / Mathlab accounts
+
| 2010.01.25 || '''First Day of Class''' <br> Group Study || Organizational Meeting / '''Mathlab accounts'''
 
|-
 
|-
−
| 2009.01.28 || Group Study || Visualization software demo #1, Misc unix skills  
+
| 2010.01.27 || Group Study || Visualization software #1, Misc unix skills <br> VMD, MOE, Chimera, vi, general unix cmds, shell scripting
 
|-
 
|-
−
| 2009.02.02 || Group Study || Visualization software demo #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 <br> '''Seawulf accounts'''
 
|-
 
|-
−
| 2009.02.04 || Group Study || Visualization software demo #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 <br> '''Seawulf accounts'''
 
|-
 
|-
−
| 2009.02.09 || Group Study || Tutorials: Group 1=DOCK, Group 2=AMBER
+
| 2010.02.08 || Group Study || Tutorials: Group 1=DOCK, Group 2=AMBER <br> project discussion
 
|-
 
|-
−
| 2009.02.11 || Group Study || Tutorials: Group 1=DOCK, Group 2=AMBER
+
| 2010.02.10 || Group Study || Tutorials: Group 1=DOCK, Group 2=AMBER <br> project discussion
 
|-
 
|-
−
| 2009.02.16 || Group Study || Tutorials: Group 1=DOCK, Group 2=AMBER
+
| 2010.02.15 || Group Study || Tutorials: Group 1=DOCK, Group 2=AMBER <br> project discussion
 
|-
 
|-
−
| 2009.02.18 || Group Study || Tutorials: Group 1=AMBER, Group 2=DOCK / Project Discussion
+
| 2010.02.17 || Group Study || Tutorials: Group 1=DOCK, Group 2=AMBER <br> project discussion
 
|-
 
|-
−
| 2009.02.23 || Group Study || Tutorials: Group 1=AMBER, Group 2=DOCK / Project Discussion
+
| 2010.02.22 || Group Study || Tutorials: Group 1=AMBER, Group 2=DOCK <br> project discussion
 
|-
 
|-
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| 2009.02.25 || Group Study || Tutorials: Group 1=AMBER, Group 2=DOCK / Project Discussion
+
| 2010.02.24 || Group Study || Tutorials: Group 1=AMBER, Group 2=DOCK <br> project discussion
 
|-
 
|-
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| 2009.03.02 || Group Study || Snow Day
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| 2010.03.01 || Group Study || Tutorials: Group 1=AMBER, Group 2=DOCK <br> project discussion
 
|-
 
|-
−
| 2009.03.04 || Group Study || Seawulf Accounts / Scripting / Project Discussion
+
| 2010.03.03 || Group Study || Tutorials: Group 1=AMBER, Group 2=DOCK <br> project discussion
 
|-
 
|-
−
| 2009.03.09 || Group Study || Project Discussion / Troubleshooting  
+
| 2010.03.08 || Group Study || Project Setups / Troubleshooting  
 
|-
 
|-
−
| 2009.03.11 || Group Study || Project Discussion / Troubleshooting  
+
| 2010.03.10 || Group Study || Project Setups / 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 || Group Study || Project Setups / Troubleshooting
 
|-
 
|-
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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 || Group Study || Project Setups / Troubleshooting
 
|-
 
|-
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| 2009.03.23 || Paiva, Fabiana ; Ray, Navamita || Folding the Ten-Amino Acid Protein CLN025 ; Crossdocking Studies of Estrogen Receptors
+
| 2010.03.22 || Group Study || Project Setups / Troubleshooting
 
|-
 
|-
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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 || Group Study || Project Setups / Troubleshooting
 
|-
 
|-
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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 || Adler, Jeremy; Chang, Andrew || Talk Title ; Talk Title
 
|-
 
|-
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| 2009.04.08 || SPRING BREAK || NO CLASS
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| 2010.04.07 || Cheglikov, Alex; Cheng-Tsung, Eric || The design of novel modulators of actin assembly; Interaction between InhA and it's inhibitors
 +
|-
 +
| 2010.04.12 || Gorgani, Farzan; Hauser, Kevin; || Talk Title ; mTER
 
|-
 
|-
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| 2009.04.13 || Steitz, Josh ; Group Study || Docking studies of Taxol and Taxol Analogs
+
| 2010.04.14 || Jiang, Lingling; Kirkup, Colleen|| Pharmacophore modeling based on Docking and MD for the inhibition of Gp41 ; Talk Title
 
|-
 
|-
−
| 2009.04.15 || Holden, Patrick ; Group Study || An Investigation of the "Relaxed-Complex" Docking Scheme Using Acetylcholinesterease
+
| 2010.04.19 || Li, Haoquan; Neckles, Carla|| Talk Title ; Computational Studies of Thiolactomycin and KasA from the FASII Pathway in Mycobacterium tuberculosis
 
|-
 
|-
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| 2009.04.20 || Paiva, Fabiana; '''Preliminary Report due''' || Folding the Ten-Amino Acid Protein CLN025
+
| 2010.04.21 || '''Preliminary Report Due''' <br> Adler, Jeremy; Chang, Andrew || Talk Title ; Talk Title
 
|-
 
|-
−
| 2009.04.22 || Ray, Navamita || Crossdocking studies of Estrogen Receptors
+
| 2010.04.26 || Cheglikov, Alex; Cheng-Tsung, Eric || Talk Title ; Interaction between InhA and it's inhibitors
 
|-
 
|-
−
| 2009.04.27 || Ali, Wahida ; Wang, Hui || Strand Slippage in DNA pol lambda ; MD simulation of hp35
+
| 2010.04.28 || Gorgani, Farzan; Hauser, Kevin; || determining the conformation of changes of hnox ; Mechanics and Dynamics of a Mitochondrial Transcription Terminator
 
|-
 
|-
−
| 2009.04.29 || LeBarron, Jamie; Dong, Xu || MD Simulations of Membrane-bound Rhodopsin ; Virtual Screening Targeting Acetylcholinesterease
+
| 2010.05.03 || Jiang, Lingling; Kirkup, Colleen|| Pharmacophore modeling based on Docking and MD for the inhibition of Gp41; Talk Title 
 
|-
 
|-
−
| 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
+
| 2010.05.05 || '''Last Day of Class''' <br> Li, Haoquan; Neckles, Carla|| Early Stages of Damage Recognition of human 8-oxoguanine glycosylase; Computational Studies of Thiolactomycin and KasA from the FASII Pathway in Mycobacterium tuberculosis
 
|-
 
|-
−
| 2009.05.06 || Group Study; '''Last Day of Class''' || Project Discussion
+
| 2010.05.12 || '''Final written report due by 5PM, May 12, 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'''
−
|-
 
−
| 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'''
 
 
|-
 
|-
 
|}
 
|}

Latest revision as of 16:23, 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 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 First Day of Class
Group Study 		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
Seawulf accounts
2010.02.03 Group Study Visualization software #3, Misc unix skills
VMD, MOE, Chimera, vi, general unix cmds, shell scripting
Seawulf accounts
2010.02.08 Group Study Tutorials: Group 1=DOCK, Group 2=AMBER
project discussion
2010.02.10 Group Study Tutorials: Group 1=DOCK, Group 2=AMBER
project discussion
2010.02.15 Group Study Tutorials: Group 1=DOCK, Group 2=AMBER
project discussion
2010.02.17 Group Study Tutorials: Group 1=DOCK, Group 2=AMBER
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 Tutorials: Group 1=AMBER, Group 2=DOCK
project discussion
2010.03.03 Group Study Tutorials: Group 1=AMBER, Group 2=DOCK
project discussion
2010.03.08 Group Study Project Setups / Troubleshooting
2010.03.10 Group Study Project Setups / Troubleshooting
2010.03.15 Group Study Project Setups / Troubleshooting
2010.03.17 Group Study Project Setups / Troubleshooting
2010.03.22 Group Study Project Setups / Troubleshooting
2010.03.24 Group Study Project Setups / Troubleshooting
2010.03.29 SPRING BREAK NO CLASS
2010.03.31 SPRING BREAK NO CLASS
2010.04.05 Adler, Jeremy; Chang, Andrew Talk Title ; Talk Title
2010.04.07 Cheglikov, Alex; Cheng-Tsung, Eric The design of novel modulators of actin assembly; Interaction between InhA and it's inhibitors
2010.04.12 Gorgani, Farzan; Hauser, Kevin; Talk Title ; mTER
2010.04.14 Jiang, Lingling; Kirkup, Colleen Pharmacophore modeling based on Docking and MD for the inhibition of Gp41 ; Talk Title
2010.04.19 Li, Haoquan; Neckles, Carla Talk Title ; Computational Studies of Thiolactomycin and KasA from the FASII Pathway in Mycobacterium tuberculosis
2010.04.21 Preliminary Report Due
Adler, Jeremy; Chang, Andrew 		Talk Title ; Talk Title
2010.04.26 Cheglikov, Alex; Cheng-Tsung, Eric Talk Title ; Interaction between InhA and it's inhibitors
2010.04.28 Gorgani, Farzan; Hauser, Kevin; determining the conformation of changes of hnox ; Mechanics and Dynamics of a Mitochondrial Transcription Terminator
2010.05.03 Jiang, Lingling; Kirkup, Colleen Pharmacophore modeling based on Docking and MD for the inhibition of Gp41; Talk Title
2010.05.05 Last Day of Class
Li, Haoquan; Neckles, Carla		 Early Stages of Damage Recognition of human 8-oxoguanine glycosylase; Computational Studies of Thiolactomycin and KasA from the FASII Pathway in Mycobacterium tuberculosis
2010.05.12 Final written report due by 5PM, May 12, 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
Retrieved from "https://ringo.ams.stonybrook.edu/index.php?title=2010_AMS-536_Spring&oldid=8025"