CSSB: In the News
Georgia Tech Researchers Probe the Physics of 'Promiscuous' Proteins
(genomeweb.com, February 2011) In order to understand protein-protein interactions, researchers face the challenge of parsing out the actual physical interfaces at which they occur — and not all proteins behave according to the rules. Jeffrey Skolnick, director of the Center for the Study of Systems Biology at the Georgia Institute of Technology, and his colleagues are studying "promiscuous" proteins — those that misbehave and bind to many other proteins in addition to their intended targets. In what they say is the first systematic study of the nature of protein-protein interfaces, Skolnick and his team have uncovered more than 1,000 structurally distinct protein-protein interactions that hinge on the underlying physics of the proteins themselves. Their work was published in PNAS in December.
Study Analyzes Protein-Protein Interactions
(softpedia.com, December 15, 2010) All the important cellular processes can only take place following interactions amidst proteins, experts know, and so the nature of those interactions is something that we simply must know. A group of scientists has now produced a new method of investigating these connections.
New Study Classifies and Analyzes Protein-Protein Interfaces
(gtresearchnews.gatech.edu, December 15, 2010) Interactions between proteins are at the heart of cellular processes, and those interactions depend on the interfaces where the direct physical contact occurs. A new study published this week suggests that there may be roughly a thousand structurally-distinct protein-protein interfaces -- and that their structures depend largely on the simple physics of the proteins.
Cracking Cellular Motion
(American Scientist, January-February 2011, Volume 99, Number 1, Page: 28) By applying biophysical principles to a simulated slice of a cell, researchers uncover molecular speed limits.
Close Quarters
(Chemical & Engineering News, November 29, 2010) Picture yourself in a subway car. When you’re alone or with only a few other passengers, raising your arm to grab an overhead strap or to look at your watch is easy. But in a packed train at rush hour, such simple motions aren’t so easy. Inside cells, proteins face crowded conditions similar to those in that rush-hour train, but scientists have traditionally studied proteins in dilute solutions, as if they had the car to themselves.
Cellular Wakes and Eddies Slow Down Molecules
(NIGMS Biomedical Beat, November 17, 2010) Like a busy shipping port, cells are crowded with different molecules that maneuver around each other to reach their destination. So what physical forces have the most impact on these molecular movements? A new simulation suggests that it's the wakes and eddies the molecules generate as they move through the cellular water. The results come from a small-scale study—15 types of molecules packed at realistic concentrations inside a model E. coli cell—but they set the stage for whole-cell simulations to study everything from cell division to drug side effects.
F1000 Weekly Roundup
(f1000.com, October 13, 2010) On the subject of protein structures, it’s often (if not usually) necessary to compare the structure you’ve just solved with the database of protein structures. While is is a pretty standard thing to do, comparing protein-protein interfaces can be just as important, but tools to do this are not so common. Enter iAlign, “a method for the structural comparison of protein–protein interfaces”3. The paper isn’t open access, but the software is available for free at http://cssb.biology.gatech.edu/iAlign (and there’s a web interface too). Me, I’m still hoping for the iSolve iPhone app.
Cellular Traffic: Modeling Shows that Factors Beyond Crowding Affect How Molecules Interact Within Cells
(gtresearchnews.gatech.edu, October 11, 2010) Using large-scale computer simulations, researchers at the Georgia Institute of Technology have identified the most important factors affecting how molecules move through the crowded environment inside living cells. The findings suggest that perturbations caused by hydrodynamic interactions – similar to what happens when the wake from a large boat affects smaller boats on a lake – may be the most important factor in this intracellular diffusion.
New MYRIAD Computer Cluster
(HPCwire.com, May 25th, 2010) Penguin Computing, experts in high performance computing (HPC) solutions, today announced that it has built one of the world's largest supercomputers for the Center for the Study of Systems Biology at the Georgia Institute of Technology (Georgia Tech), one of the leading research universities in the U.S. Ranking within the top 100 supercomputers in the world, Georgia Tech's massive MYRIAD cluster comprises over 10,000 CPU cores with a 100 TFLOP (teraflop) theoretical maximum performance.
Computer predicts anti-cancer molecules

(UPI.com, June 17, 2008) U.S. scientists have created a computerized method of analyzing cellular activity that correctly predicts the anti-tumor activity of several molecules.

Researchers Jeffrey Skolnick and John McDonald led a Georgia Institute of Technology team in developing the tool, called CoMet, that studies the integrated machinery of the cell, predicting which components can have an effect on cancer.