Lehigh University
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Making a Game of Molecule Manipulation

Lehigh researcher Brian Chen just wants everyone to get along. A computer scientist who focuses on the structure and behavior of biological machines, his work informs biologists about the behavior of the minute systems that make up a living body.

Chen, an assistant professor in the Department of Computer Science and Engineering, is working with a new software startup called Leap Motion, which may change the way engineers and biologists work together. The images in the accompanying video might just look like a CGI effect, but Chen hopes the tool will make it easier for biologists to manipulate molecules on the fly, speeding research into protein behavior and drug development.

“It will be more accessible to biologists who might be interested in using computational tools but might not have the background in order to use a lot of those devices,” he said.

 
Today’s superior computational power allows researchers like Chen to play with virtual molecules and biological systems. The stickiest part of handling virtual molecules is picking out single atoms among thousands of molecular building blocks. Using traditional software, a structural biologist who wants to simulate changes to the digestive enzyme trypsin, for example, would have to spend time implementing the necessary code. The computer would spit out numeric or other non-visual data that the biologist would have to interpret.

The software Chen is working with, on the other hand, might be modified to give biologists a richer, more visual interaction with molecular images. Instead of just showing an image onscreen however, the interface would integrate analytical data with an image. Chen said he's still working out the specifics, but additional views may illustrate specific interactions for specific atoms. Though trypsin would be represented by 1,500 to 2,000 atoms – a large number to track by any means – the user would be able to interrogate each atom about how it affects trypsin activity.

With his hands hovering over the Leap Motion Controller, a device not much bigger than a USB stick drive, Chen demonstrates how it uses an infrared camera to capture and mimic his hand motions onscreen in real time. A pair of ghostly glowing hands echoes every subtle, 3-dimensional movement, and gestures such as pointing and waving. The virtual hands would help the biologist examine the molecule from specific angles, add and remove atoms, and experiment with new bonds.

“The great thing about the Leap Motion device is that it’s very fast, it’s very accurate, and it’s also very cheap,” Chen said. It could work with software tailored to any discipline that requires intuitive manipulation of complex structures, Chen said.

“One thing that people are doing is looking at these structures and asking questions like, how would this structure fit into another structure? They’re trying to answer really basic questions about single molecules that make biological systems work,” Chen said. For example, why don't some drug targets in HIV respond to some HIV drugs?

Though it’s not yet specialized for specific applications, the software has the potential to help biologists find the answer and put them a step closer to halting diseases like HIV in their tracks.

Story by Manasee Wagh

Posted on Friday, August 30, 2013

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