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Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home

2007; Wiley; Volume: 69; Issue: S8 Linguagem: Inglês

10.1002/prot.21636

1097-0134

Rhiju Das, Bin Qian, Srivatsan Raman, Robert M. Vernon, James Thompson, Philip Bradley, Sagar D. Khare, Michael D. Tyka, Divya Bhat, Dylan Chivian, David E. Kim, William Sheffler, Lars Malmström, Andrew M. Wollacott, Chu Wang, Ingemar André, David Baker,

Medical Imaging Techniques and Applications

We describe predictions made using the Rosetta structure prediction methodology for both template-based modeling and free modeling categories in the Seventh Critical Assessment of Techniques for Protein Structure Prediction. For the first time, aggressive sampling and all-atom refinement could be carried out for the majority of targets, an advance enabled by the [email protected] distributed computing network. Template-based modeling predictions using an iterative refinement algorithm improved over the best existing templates for the majority of proteins with less than 200 residues. Free modeling methods gave near-atomic accuracy predictions for several targets under 100 residues from all secondary structure classes. These results indicate that refinement with an all-atom energy function, although computationally expensive, is a powerful method for obtaining accurate structure predictions. Proteins 2007. © 2007 Wiley-Liss, Inc.