Difference between revisions of "2013 AMS-536 Spring"

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(Created page with "<br> {| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%" |- style="background:white" ! style="width:10%" | '''Ins...")
 
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| 2012.01.23 || '''First Day of Class and Organizational Meeting''' <br> Group Study || Mathlab account setups, Unix and vi tutorials <br> (1) http://www.ee.surrey.ac.uk/Teaching/Unix <br> (2) At Linux command prompt type "vimtutor" (without the quotes) to start a built in tutorial for the text editor program called vi
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| 2012.01.28 || '''First Day of Class and Organizational Meeting''' <br> Group Study || Mathlab account setups, Unix and vi tutorials <br> (1) http://www.ee.surrey.ac.uk/Teaching/Unix <br> (2) At Linux command prompt type "vimtutor" (without the quotes) to start a built in tutorial for the text editor program called vi
 
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| 2012.01.25 || Group Study || Continue Mathlab account setups, Unix and vi tutorials <br> (1) http://www.ee.surrey.ac.uk/Teaching/Unix <br> (2) At Linux command prompt type "vimtutor" (without the quotes) to start a built in tutorial for the text editor program called vi  
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| 2012.01.30 || Group Study || Continue Mathlab account setups, Unix and vi tutorials <br> (1) http://www.ee.surrey.ac.uk/Teaching/Unix <br> (2) At Linux command prompt type "vimtutor" (without the quotes) to start a built in tutorial for the text editor program called vi  
 
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| 2012.01.30 || Group Study || Visualization/analysis software, <br> VMD, MOE, Chimera, <br> Seawulf account setups, environments, shell scripting, misc unix
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| 2012.02.04 || Group Study || Visualization/analysis software, <br> VMD, MOE, Chimera, <br> Seawulf account setups, environments, shell scripting, misc unix
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| 2012.02.01 || Group Study || Visualization/analysis software, <br> VMD, MOE, Chimera, <br> Seawulf account setups, environments, shell scripting, misc unix
 
 
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| 2012.02.06 || Group Study || Visualization/analysis software, <br> VMD, MOE, Chimera, <br> Seawulf account setups, environments, shell scripting, misc unix
 
| 2012.02.06 || Group Study || Visualization/analysis software, <br> VMD, MOE, Chimera, <br> Seawulf account setups, environments, shell scripting, misc unix
 
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| 2012.02.08 || Group Study || Cheat Sheet: [[Unix]], [[Vi]], [[C_Shell_Scripting]]
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| 2012.02.11 || Group Study || Visualization/analysis software, <br> VMD, MOE, Chimera, <br> Seawulf account setups, environments, shell scripting, misc unix
 
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| 2012.02.13 || Group Study || Tutorials: DOCK <br> individual project discussion [http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2012.02.13.ams536.joe.docking_intro.pdf Allen, W.]
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| 2012.02.13 || Group Study || Cheat Sheet: [[Unix]], [[Vi]], [[C_Shell_Scripting]]
 
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| 2012.02.15 || Group Study || Tutorials: DOCK <br> individual project discussion
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| 2012.02.18 || Group Study || Tutorials: DOCK <br> individual project discussion [http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2012.02.13.ams536.joe.docking_intro.pdf Allen, W.]
 
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| 2012.02.20 || Group Study || Tutorials: DOCK <br> individual project discussion
 
| 2012.02.20 || Group Study || Tutorials: DOCK <br> individual project discussion
 
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| 2012.02.22 || Group Study || Tutorials: DOCK <br> individual project discussion
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| 2012.02.25 || Group Study || Tutorials: DOCK <br> individual project discussion
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| 2012.02.27 || Group Study || Tutorials: DOCK <br> individual project discussion
 
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| 2012.02.27 || Group Study || Tutorials: DOCK <br> wiki editing
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| 2012.03.04 || Group Study || Tutorials: DOCK <br> wiki editing
 
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| 2012.02.29 || Group Study || Tutorials: AMBER <br> individual project discussion [http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2012.02.29.ams536.lingling.amber_intro.pdf Jiang L.]
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| 2012.03.06 || Group Study || Tutorials: AMBER <br> individual project discussion [http://rizzo.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  
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| 2012.03.11 || Group Study || Tutorials: AMBER <br> individual project discussion  
 
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| 2012.03.07 || Group Study || Tutorials: AMBER <br> individual project discussion  
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| 2012.03.13 || Group Study || Tutorials: AMBER <br> individual project discussion  
 
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| 2012.03.12 || Group Study || Tutorials: AMBER <br> individual project discussion
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| 2012.03.18 || Spring Recess || Spring Recess
 
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| 2012.03.14 || Group Study || Tutorials: AMBER <br> wiki editing
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| 2012.03.20 || Spring Recess || Spring Recess
 
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| 2012.03.19 || Group Study || Project Setups / Troubleshooting
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| 2012.03.25 || Group Study || Tutorials: AMBER <br> individual project discussion
 
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| 2012.03.21 || Group Study || Project Setups / Troubleshooting
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| 2012.03.27 || Group Study || Tutorials: AMBER <br> wiki editing
 
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| 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
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| 2012.04.01 || Group Study || Project Setups / Troubleshooting
 
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| 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
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| 2012.04.03 || Group Study || Project Setups / Troubleshooting
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| 2012.04.02 || Spring Recess || Spring Recess
 
 
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| 2012.04.04 || Spring Recess || Spring Recess
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| 2012.04.08 || TBD || Project Proposal
 
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| 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
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| 2012.04.10 || TBD || Project Proposal
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| 2012.04.15 || TBD || Project Proposal
 
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| 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
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| 2012.04.17 || '''Preliminary Report Due''' <br> TBD || Project Proposal
 
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| 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
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| 2012.04.22 || TBD || Project Proposal
 
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| 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
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| 2012.04.24 || TBD || Progress Report
 
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| 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  
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| 2012.04.29 || TBD || Progress Report  
 
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| 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
+
| 2012.05.01 || TBD || Progress Report
 
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|-
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| 2012.04.30 || Shi, Hui; Sinayev, Roman || Identification of potent inhibitors for human epidermal fatty acid binding protein ; De Novo Search
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| 2012.05.06 || TBD || Progress Report
 
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| 2012.05.02 || '''Last Day of Class''' <br> 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
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| 2012.05.08 || '''Last Day of Class''' <br> TBD || Progress Report
 
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| 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'''
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| 2012.05.15 || '''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'''
 
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Revision as of 11:21, 14 January 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
2012.01.28 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
2012.01.30 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
2012.02.04 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
2012.02.11 Group Study Visualization/analysis software,
VMD, MOE, Chimera,
Seawulf account setups, environments, shell scripting, misc unix
2012.02.13 Group Study Cheat Sheet: Unix, Vi, C_Shell_Scripting
2012.02.18 Group Study Tutorials: DOCK
individual project discussion Allen, W.
2012.02.20 Group Study Tutorials: DOCK
individual project discussion
2012.02.25 Group Study Tutorials: DOCK
individual project discussion
2012.02.27 Group Study Tutorials: DOCK
individual project discussion
2012.03.04 Group Study Tutorials: DOCK
wiki editing
2012.03.06 Group Study Tutorials: AMBER
individual project discussion Jiang L.
2012.03.11 Group Study Tutorials: AMBER
individual project discussion
2012.03.13 Group Study Tutorials: AMBER
individual project discussion
2012.03.18 Spring Recess Spring Recess
2012.03.20 Spring Recess Spring Recess
2012.03.25 Group Study Tutorials: AMBER
individual project discussion
2012.03.27 Group Study Tutorials: AMBER
wiki editing
2012.04.01 Group Study Project Setups / Troubleshooting
2012.04.03 Group Study Project Setups / Troubleshooting
2012.04.08 TBD Project Proposal
2012.04.10 TBD Project Proposal
2012.04.15 TBD Project Proposal
2012.04.17 Preliminary Report Due
TBD 		Project Proposal
2012.04.22 TBD Project Proposal
2012.04.24 TBD Progress Report
2012.04.29 TBD Progress Report
2012.05.01 TBD Progress Report
2012.05.06 TBD Progress Report
2012.05.08 Last Day of Class
TBD 		Progress Report
2012.05.15 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
Retrieved from "https://ringo.ams.stonybrook.edu/index.php?title=2013_AMS-536_Spring&oldid=7678"