Difference between revisions of "2008 AMS-536 Spring"
From Rizzo_Lab
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== Final Written Project Information == | == Final Written Project Information == | ||
| − | *[http:// | + | *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.guidelines.pdf project.guidelines.pdf] |
| − | *[http:// | + | *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.example.dGhyd.pdf project.example.dGhyd.pdf] |
| − | *[http:// | + | *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.example.MMPS.pdf project.example.MMPS.pdf] |
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== Tutorials, Software Links, and Other Relevant Class Information== | == Tutorials, Software Links, and Other Relevant Class Information== | ||
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| 2008.05.12 || Oum, Yoon Hyeun || Calculation of Binding Affinities for Adenovirus Knob protein with CAR Receptor from MD Simulation | | 2008.05.12 || Oum, Yoon Hyeun || Calculation of Binding Affinities for Adenovirus Knob protein with CAR Receptor from MD Simulation | ||
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| − | | 2008.05.14 || Final written report due by 5PM today. Late papers will not be accepted. See http:// | + | | 2008.05.14 || Final written report due by 5PM today. Late papers will not be accepted. See http://ringo.ams.sunysb.edu (go to teaching) for detailed guidelines and sample reports. || Place hard copy in Rizzo mailbox (near AMS offices Math Tower first floor) and email electronic copy to rizzorc@gmail.com |
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Revision as of 16:20, 5 August 2013
| Instructor | Dr. Robert C. Rizzo [631-632-8519, rizzorc@gmail.com] |
|---|---|
| Course No. | AMS-536 |
| Location/Time | Math Tower, Room 1-122, Fridays 2:20-3:40 pm |
| Office Hours | Anytime or by appointment, Room 1-101, Dept. of Applied Math & Statistics |
Final Written Project Information
Tutorials, Software Links, and Other Relevant Class Information
Schedule
Note: Each participant please update the Wiki as required
| Date | Participant | Talk |
| 2008.01.28 | Group Study | Organizational Meeting / Mathlab accounts |
| 2008.01.30 | Group Study | Visualization software demo #1 |
| 2008.02.04 | Group Study | Visualization software demo #2 |
| 2008.02.06 | Group Study | Tutorials: Group 1=DOCK, Group 2=AMBER |
| 2008.02.11 | Group Study | Tutorials: Group 1=DOCK, Group 2=AMBER |
| 2008.02.13 | Group Study | Tutorials: Group 1=DOCK, Group 2=AMBER |
| 2008.02.18 | Group Study | Tutorials: Group 1=AMBER, Group 2=DOCK |
| 2008.02.20 | Group Study | Tutorials: Group 1=AMBER, Group 2=DOCK |
| 2008.02.25 | Group Study | Tutorials: Group 1=AMBER, Group 2=DOCK |
| 2008.02.27 | Goyal, Rashi ; Group Study | Targeted Drug Design for Pandemic Influenza ; Seawulf Accounts |
| 2008.03.03 | Group Study | Seawulf Accounts / Scripting /Sofware compilation |
| 2008.03.05 | Group Study | Seawulf Accounts / Scripting/ Sofware compilation |
| 2008.03.10 | McGillick, Brian ; Group Study | Using Computation to Elicit the Structure of the HIVgp41 Fusion Peptide; Seawulf Accounts / Scripting/ Sofware compilation |
| 2008.03.12 | Barsegian, Garen ; Palmer, Lance | Inhibitor binding to MMPs ; Interaction of Borrelia OspB protein with a Bactericidal Antibody |
| 2008.03.17 | Spring Recess | No Class |
| 2008.03.19 | Spring Recess | No Class |
| 2008.03.24 | Huang, Yulin ; Group Discussion | EGFR/Cross Docking ; Group Discussion |
| 2008.03.26 | Berger, William ; Hai, Nguyen Minh | Introduction to Ftsz and Proposed MD Simulations ; Understanding low-frequency motions in protein helps to enhance sampling efficiency. |
| 2008.03.31 | Liu, Yang ; Martinez, Carmenza | MD simulation on 11-mer DNA duplex with etheno-dG ; MD simulations on Trp Cage |
| 2008.04.02 | Oum, Yoon Hyeun ; Goyal, Rashi | Simulation for interaction of Adenovirus Knob with CAR ; Targeted Drug Design for Pandemic Influenza |
| 2008.04.07 | McGillick, Brian ; Barsegian, Garen | Using Computation to Elicit the Structure of the HIVgp41 Fusion Peptide ; Inhibitor binding to MMPs |
| 2008.04.09 | Palmer, Lance ; Huang, Yulin | Interaction of Borrelia OspB protein with a Bactericidal Antibody ; EGFR Cross-Docking Results |
| 2008.04.14 | Berger, William; Hai, Nguyen Minh | Ftsz Dimer MD Simulation Initial Results; Compare Trp-cage MD and REMD simulation results |
| 2008.04.16 | Liu, Yang ; Martinez, Carmenza | MD simulation on 11-mer DNA duplex with etheno-dG ; MD simulations on Trp Cage |
| 2008.04.21 | Passover | No Class |
| 2008.04.23 | Oum, Yoon Hyeun ; Goyal, Rashi | MD Simulations for the interaction of Adenovirus Knob and Receptor with NAMD ; Targeted Drug Design for Pandemic Influenza |
| 2008.04.28 | McGillick, Brian ; Barsegian, Garen | Using Computation to Elicit the Structure of the HIVgp41 Fusion Peptide ; Inhibitor binding to MMPs |
| 2008.04.30 | Palmer, Lance ; Huang, Yulin | Interaction of Borrelia OspB protein with a Bactericidal Antibody ; EGFR/Cross Docking |
| 2008.05.05 | Berger, William ; Hai, Nguyen Minh | Molecular Dynamics study of Ftsz dimer conformation induced by the γ-phosphate of bound nucleotide ; Compare Trp-cage MD and REMD simulation results |
| 2008.05.07 | Liu, Yang ; Martinez, Carmenza | MD simulation on 11-mer DNA duplex with etheno-dG ; MD simmulations for Trp Cage |
| 2008.05.12 | Oum, Yoon Hyeun | Calculation of Binding Affinities for Adenovirus Knob protein with CAR Receptor from MD Simulation |
| 2008.05.14 | Final written report due by 5PM today. Late papers will not be accepted. See http://ringo.ams.sunysb.edu (go to teaching) for detailed guidelines and sample reports. | Place hard copy in Rizzo mailbox (near AMS offices Math Tower first floor) and email electronic copy to rizzorc@gmail.com |
