Julie Forman-Kay researches proteins that do not follow a fixed three-dimensional structure. The understanding of these proteins, called intrinsically disordered proteins (IDPs), is an important part of understanding diseases such as cystic fibrosis. She has created freely available software called ENSEMBLE that allows researchers to conduct analysis of IDPs.
Describing these proteins — which are involved in many critical biological processes and a range of diseases and disorders, from cancer to autism — is challenging. So, she’s written a very computationally intensive program called ENSEMBLE, whose goal is to define ensembles of disordered protein states using experimental data. She uses Compute Canada resources for this project.
“Basically, the idea is to characterize disordered protein ensembles using experimental data,” she says. “And the big idea is to understand how disordered protein states function in biology and disease.”
In another project, which also uses Compute Canada resources, her team is investigating a large protein (mutated in cystic fibrosis) that has folded and disordered regions. “We’ve employed and developed different simulation approaches. We have a close collaborator in Israel who is on my account. We work with him on various molecular dynamics simulations and compare our ensemble structures of the disordered region and his simulations and our experimental data.”
Dr. Forman-Kay says she couldn’t do her work without Compute Canada. “It’s essential because disordered proteins are so challenging and all of the tools we’re developing are very computationally intensive because experiments alone can’t very clearly define things. You really need a huge sample of conformations. The only way to do it is with the kind of power that’s available through Compute Canada.”