The National Institutes of Health Roadmap for Medical Research has recently completed the first stage of an ambitious program to expand the computational infrastructure and software tools needed to...
Jan, 01, 2006
How can they help us understand proteins?
Graphs, or networks, have been widely adopted in computational biology, with examples including protein-protein interaction networks, gene regulatory networks, and residue interaction networks in...
Jun, 20, 2013
How increased coverage of the structure space is transforming the field of biology
When the human genome was completely sequenced in 2003, researchers were already pondering how biomedicine could make use of it. One hope was that the sequences would lead to a greater...
Jan, 01, 2010
Researchers are not simply retrieving and repackaging what is already known, but are also deriving new knowledge by discovering connections that were previously unnoticed.
Not long ago, reading biomedical literature involved hours in the library combing through rows of dusty periodicals—not to mention pocketfuls of change for the copy machine. Now, although the...
Jul, 01, 2008
OpenMM provides a common interface for doing MD simulations on GPUs
Over the last three years, the lab of Vijay Pande, PhD, at Stanford University has optimized their molecular dynamics (MD) algorithms to take advantage of the fast computing that’s possible...
Jul, 01, 2008
The complexity and variability of aging itself, along with the fragmented nature of researchers’ current understanding of aging, call for tools that can help scientists dig through mounds of data to find often subtle connections.
Jeanne Louise Calment of Arles, France rode a bicycle until she was 100 years old. When she gave up smoking at age 117, her doctor suspected it was out of pride. (She couldn’t see well enough...
Apr, 01, 2008
Using molecular dynamics (MD) software, scientists can simulate molecular movement to study biological phenomena that currently cannot be observed experimentally.
But the value of MD...
Jul, 01, 2009
AMOEBA's polarizable force field now integrated with OpenMM
Many have long hoped that molecular dynamics calculations—the computation of how molecules move and interact with other molecules—would revolutionize the world of synthetic chemistry,...
Sep, 01, 2011
Now, with just a few mouse clicks, anyone with a computer and an Internet connection can create graphic images of RNA molecules (using ToRNADo) or generate the ion environments that surround these...
Jan, 01, 2007
The fittest organisms survive and produce offspring, according to the Darwinian theory of natural selection. And the changes that make an organism fit happen at the molecular level: when genes mutate...
Oct, 01, 2007