Stony Brook Joint Group Meetings in Computational Structural Biology

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Joint Group Meetings in Computational Structural Biology convene every second Thursday of the month for one hour. There will be a 1/2 hour presentation by a member of one of the partipating research groups followed by discussion after or during the talk. The focus of the presentation is on the computational and analytical methods used to simulate biological systems as well as the problems and issues concerning these. Currently particpiating research groups are: Davenport, Deng, Green, Rizzo, Simmerling, and Wang .

Group Meeting Time and Location

5:30 to 6:30PM in Chemistry Room 410

Group Meeting Food

IMPORTANT: The group that is presenting is also is responsible for bringing pizza and soda. We have been ordering seven pizzas (cut into 8 slices) from SAC and bringing three 2-liter bottles of soda. Don't forget plates, napkins, and cups.

SAC pizza needs to be ordered in advance, preferably the day before the meeting. Go to the SAC cafeteria office, just past the entrance door. You can order the pizza there and pay with a credit card. Insist on NOT paying sales sax since it will not be reimbursed. If they give you a hassle tell them to do it anyway and they will agree. Get the receipt then, or make sure that someone gets the receipt when they pick up the pizza later. Since they don't have large soda bottles, you need to get these somewhere else. Reminder- don't forget plates, napkins, and cups!

Also, since each group will need to get reimbursed by their respective departments it is important to save all receipts.

Group Meeting Schedule

Each group is responsible for updating the Joint Group Meeting Wiki.

Date Speaker Group Talk Title
13th Nov 2007 Dan Roe Simmerling Replica Exchange
11th Dec 2007 Kun Song and Christina Bergonzo Simmerling Umbrella Sampling and Nudged Elastic Band Methods
12th Feb 2008 Sudipto Mukherjee Rizzo Docking Testset and Improvements in Docking Protocol
11th Mar 2008 Vadim Patsalo Green Design and Synthesis of Minimal and Persistent Protein Complexes
08th Apr 2008 Yongzhi Chen Deng Task Mapping Schemes for Parallel Computing
13th May 2008 AJ Campbell Simmerling Parameterization of Damaged DNA for Molecular Dynamics Studies
10th Jun 2008 Yolanda Small Davenport Molecular Dynamics Simulations of Cellulose Degrading Enzymes
08th Jul 2008 Trent Balius Rizzo Inhibition and Conformational Shifts of EGFR Tyrosine Kinase Domain Using Molecular Dynamics
12th Aug 2008 Chris Marai Wang Studies of NTL9 Protein Unfolding
09th Sep 2008 Yukiji Fujimoto Green Carbohydrate recognition by antiviral lectins
16th Oct 2008 Christina Bergonzo Simmerling Combining coarse grained models and atomistic MD simulations to accelerate slow motions
13th Nov 2008 Jim Davenport Davenport Density Functional Theory
11th Dec 2008 - - No Meeting: AMS Holiday Party
08th Jan 2009 Brian McGillick Rizzo HIVgp41 and lipid bilayer simulations
12th Feb 2009 Reid Powell Deng Mapping-Oriented Network Analysis for Supercomputers
12th Mar 2009 Noel Carrascal Green -
09th Apr 2009 - Wang -
14th May 2009 Amber Carr Simmerling Examining the Effect of Self-guided Langevin Dynamics on the Thermodynamic Stability and Kinetics of Peptide Folding
11th Jun 2009 Summer Time -
09th Jul 2009 Summer Time -
13th Aug 2009 Summer Time -
10th Sep 2009 Postdoc candidate Simmerling -
8th Oct 2009 Yulin Huang Rizzo Targeted design of dual kinase inhibitors for breast cancer
19th Nov 2009 Fred Feng Deng Molecular Dynamics Simulation of Blood Flows Using Supercomputers
10th Dce 2009 - Green -
14th Jan 2009 - Fernandez-Serra -
11th Feb 2010 - Wang -
11th Mar 2010 - Simmerling -
8th Apr 2010 - Rizzo -
6th May 2010 - Deng -