Molecular Dynameomics

A 2005 INCITE Project

This project, led by by Valerie Daggett of the University of Washington, was awarded 2 million processor-hours. The project will combine molecular dynamics and proteomics to create an extensive repository of the molecular dynamics structures for protein folds, including the unfolding pathways. According to Daggett, there are approximately 1,130 known, non-redundant protein folds, of which her group has simulated about 30. She plans to use the information from these simulations to improve algorithms for predicting protein structure.

"Structure prediction remains one of the elusive goals of protein chemistry," Daggett wrote in her INCITE proposal. "It is necessary to successfully predict native states of proteins, in order to translate the current deluge of genomic information into a form appropriate for better functional identification of proteins and drug design."

After hearing that her proposal was one of three to receive an INCITE allocation, Daggett said, "We are excited about the massive resources we will have access to now. Our project will run literally hundreds and hundreds of simulations, each a little different, so we will be running a lot of smaller jobs all at once, using up to 1,000 processors at a time."