RNA Builder User Profile: Rick Russell, PhD

Through RNABuilder, Simbios brings computational modeling to Rick Russell’s lab at the University of Texas.

from http://biomedicalcomputationreview.org/content/simbios-bringing-biomedical-simulation-your-fingertips


Rick Russell, PhD, associate professor of chemistry and biochemistry at the University of Texas, Austin, studies RNA structure formation in the laboratory. Recognizing that his experimental data were not sufficient to give a structural picture of RNA folding, he decided to turn to modeling for help. Last winter, he asked graduate student Yaqi Wan to scour the Internet for RNA modeling tools. She tried for a few weeks but found nothing that was user-friendly enough for a graduate student without training.


Fortunately, in the spring, Sam Flores, PhD, a post-doc in Simbios, visited Russell’s lab to demonstrate Simbios’ RNABuilder software (see Biomedical Computation Review, Summer 2009, p.32), which can quickly model possible RNA structures based on limited experimental information. “We immediately saw this as the opportunity we were looking for,” Russell says.


Since then, Wan has learned how to use RNABuilder and is helping Flores add functionality to the software—allowing it to model RNAs based on homology to related RNAs. “That hadn’t been done before with RNABuilder and really hadn’t been done much for RNA at all,” says Russell.  Russell and Wan then successfully used this new capability on a test case, generating a model of a fairly complex, 200-nucleotide RNA without reference to the known crystal structure. They plan to use RNABuilder to model a related RNA for which the structure of extensive regions is unknown.


“This is basically a first for my lab, to work with computational models,” Russell says.  “It's quite helpful to have such knowledgeable and interactive collaborators.”

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