Difference between revisions of "2012 AMS-536 Spring"

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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/projectA.student.info.doc project.student.info.doc]
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*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/projectA.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]
 
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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
 
|-
 
|-
−
| 2012.02.08 || Group Study || Tutorials: AMBER <br> individual project discussion
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| 2012.02.08 || Group Study || Cheat Sheet: [[Unix]], [[Vi]], [[C_Shell_Scripting]]
 
|-
 
|-
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| 2012.02.13 || Group Study || Tutorials: AMBER <br> individual project discussion
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| 2012.02.13 || Group Study || Tutorials: DOCK <br> individual project discussion [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2012.02.13.ams536.joe.docking_intro.pdf Allen, W.]
 
|-
 
|-
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| 2012.02.15 || Group Study || Tutorials: AMBER <br> individual project discussion
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| 2012.02.15 || Group Study || Tutorials: DOCK <br> individual project discussion
 
|-
 
|-
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| 2012.02.20 || Group Study || Tutorials: AMBER <br> individual project discussion
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| 2012.02.20 || Group Study || Tutorials: DOCK <br> individual project discussion
 
|-
 
|-
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| 2012.02.22 || Group Study || Tutorials: AMBER <br> individual project discussion
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| 2012.02.22 || Group Study || Tutorials: DOCK <br> individual project discussion
 
|-
 
|-
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| 2012.02.27 || 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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| 2012.02.29 || Group Study || Tutorials: DOCK <br> individual project discussion
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| 2012.02.29 || Group Study || Tutorials: AMBER <br> individual project discussion [http://ringo.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: DOCK <br> individual project discussion  
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| 2012.03.05 || Group Study || Tutorials: AMBER <br> individual project discussion  
 
|-
 
|-
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| 2012.03.07 || Group Study || Tutorials: DOCK <br> individual project discussion  
+
| 2012.03.07 || Group Study || Tutorials: AMBER <br> individual project discussion  
 
|-
 
|-
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| 2012.03.12 || Group Study || Project Setups / Troubleshooting
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| 2012.03.12 || Group Study || Tutorials: AMBER <br> individual project discussion
 
|-
 
|-
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| 2012.03.14 || Group Study || Project Setups / Troubleshooting
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| 2012.03.14 || Group Study || Tutorials: AMBER <br> wiki editing
 
|-
 
|-
 
| 2012.03.19 || Group Study || Project Setups / Troubleshooting
 
| 2012.03.19 || Group Study || Project Setups / Troubleshooting
 
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|-
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| 2012.03.21 || Last, First; Last, First || Talk Title ; Talk Title
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| 2012.03.21 || Group Study || Project Setups / Troubleshooting
 
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|-
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| 2012.03.26 || Last, First; Last, First || Talk Title ; Talk Title
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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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| 2012.03.28 || Last, First; Last, First || Talk Title ; Talk Title
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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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|-  
 
| 2012.04.02 || Spring Recess || Spring Recess  
 
| 2012.04.02 || Spring Recess || Spring Recess  
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| 2012.04.04 || Spring Recess || Spring Recess  
 
| 2012.04.04 || Spring Recess || Spring Recess  
 
|-
 
|-
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| 2012.04.09 || Last, First; Last, First || Talk Title ; Talk Title
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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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| 2012.04.11 || '''Preliminary Report Due''' <br> Last, First; Last, First || Talk Title ; Talk Title
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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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| 2012.04.16 || Last, First; Last, First || Talk Title ; Talk Title
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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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| 2012.04.18 || Last, First; Last, First || Talk Title ; Talk Title
+
| 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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| 2012.04.23 || Last, First; Last, First || Talk Title ; Talk Title  
+
| 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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| 2012.04.25 || Last, First; Last, First || Talk Title ; Talk Title
+
| 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
 
|-
 
|-
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| 2012.04.30 || Last, First; Last, First || Talk Title ; Talk Title
+
| 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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| 2012.05.02 || '''Last Day of Class''' <br> Last, First; Last, First || Talk Title ; Talk Title
+
| 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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| 2012.05.19 || '''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'''
+
| 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'''
 
|-
 
|-
 
|}
 
|}

Latest revision as of 16:24, 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 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
2012.01.23 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
2012.01.25 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
2012.01.30 Group Study Visualization/analysis software,
VMD, MOE, Chimera,
Seawulf account setups, environments, shell scripting, misc unix
2012.02.01 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
2012.02.08 Group Study Cheat Sheet: Unix, Vi, C_Shell_Scripting
2012.02.13 Group Study Tutorials: DOCK
individual project discussion Allen, W.
2012.02.15 Group Study Tutorials: DOCK
individual project discussion
2012.02.20 Group Study Tutorials: DOCK
individual project discussion
2012.02.22 Group Study Tutorials: DOCK
individual project discussion
2012.02.27 Group Study Tutorials: DOCK
wiki editing
2012.02.29 Group Study Tutorials: AMBER
individual project discussion Jiang L.
2012.03.05 Group Study Tutorials: AMBER
individual project discussion
2012.03.07 Group Study Tutorials: AMBER
individual project discussion
2012.03.12 Group Study Tutorials: AMBER
individual project discussion
2012.03.14 Group Study Tutorials: AMBER
wiki editing
2012.03.19 Group Study Project Setups / Troubleshooting
2012.03.21 Group Study Project Setups / Troubleshooting
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
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
2012.04.02 Spring Recess Spring Recess
2012.04.04 Spring Recess Spring Recess
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
2012.04.11 Preliminary Report Due
Shi, Hui; Sinayev, Roman 		Identification of potent inhibitors for human epidermal fatty acid binding protein ; De Novo Search
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
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
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
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
2012.04.30 Shi, Hui; Sinayev, Roman Identification of potent inhibitors for human epidermal fatty acid binding protein ; De Novo Search
2012.05.02 Last Day of Class
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
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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