The structure of RNA is an important key to its function—including its role in disease. However, the structure of most RNAs is unknown because their extreme flexibility and high charge...
Mar, 01, 2009
Confidence boost for modelers
It’s often said that all models are wrong, but some are useful. And one model that certainly falls in the “useful” category is the human lower-limb model that Scott Delp published...
Jun, 01, 2010
LoopTK samples and visualizes many conformations of a protein loop to better understand loop movement
In the gaps between the tight coils and flattened sheets that comprise most protein structures, flexible loops wave and bend. When crystallized, these loops can appear fuzzy in an electron density...
Jul, 01, 2007
Even when we simply stand still on two feet, our brains communicate with our muscles—firing them appropriately to keep us upright against gravity. So when scientists simulate simple or complex...
Jun, 06, 2012
Set objectives and follow through
Having engineered several scientific software applications for public consumption, the authors know from experience that the process offers unique challenges. Typically, the algorithms being...
Oct, 22, 2012
Researchers can now create musculoskeletal models and simulations on an open source platform. In August, Simbios researchers released OpenSim 1.0. This freely available software can, in about 20...
Oct, 01, 2007
Filling a gap in single molecule experimental work
Scientists sometimes find themselves up to their elbows in Styrofoam balls, pipe cleaners, and metal rods as they try to build models of the molecules they are studying. Now, they can exchange all...
Apr, 01, 2010
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
OpenSim 2.0 promises greater opportunities for customization
With its initial release two years ago, OpenSim offered researchers a powerful open-source application for simulating movement. Simple enough to be used by high school students yet advanced enough to...
Jan, 01, 2010
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