title: Structure prediction using sparse simulated NOE restraints with Rosetta in CASP11.
abstract: In CASP11 we generated protein structure models using simulated ambiguous and unambiguous nuclear Overhauser effect (NOE) restraints with a two stage protocol. Low resolution models were generated guided by the unambiguous restraints using continuous chain folding for alpha and alpha-beta proteins, and iterative annealing for all beta proteins to take advantage of the strand pairing information implicit in the restraints. The Rosetta fragment/model hybridization protocol was then used to recombine and regularize these models, and refine them in the Rosetta full atom energy function guided by both the unambiguous and the ambiguous restraints. Fifteen out of 19 targets were modeled with GDT-TS quality scores greater than 60 for Model 1, significantly improving upon the non-assisted predictions. Our results suggest that atomic level accuracy is achievable using sparse NOE data when there is at least one correctly assigned NOE for every residue. Proteins 2016; 84(Suppl 1):181-188. © 2016 Wiley Periodicals, Inc.
authors: Department of Biochemistry, University of Washington, Seattle, Washington, 98195.|Institute for Protein Design, University of Washington, Seattle, Washington, 98195.
authors: Sergey
authors: S
authors: Ovchinnikov
authors: Department of Biochemistry, University of Washington, Seattle, Washington, 98195.|Institute for Protein Design, University of Washington, Seattle, Washington, 98195.
authors: Hahnbeom
authors: H
authors: Park
authors: Institute for Protein Design, University of Washington, Seattle, Washington, 98195.|Howard Hughes Medical Institute, University of Washington, Seattle, Washington, 98195.
authors: David E
authors: DE
authors: Kim
authors: Department of Biochemistry, University of Washington, Seattle, Washington, 98195.|Institute for Protein Design, University of Washington, Seattle, Washington, 98195.
authors: Yuan
authors: Y
authors: Liu
authors: Department of Biochemistry, University of Washington, Seattle, Washington, 98195.|Institute for Protein Design, University of Washington, Seattle, Washington, 98195.
authors: Ray Yu-Ruei
authors: RY
authors: Wang
authors: Department of Biochemistry, University of Washington, Seattle, Washington, 98195. dabaker@u.washington.edu.|Institute for Protein Design, University of Washington, Seattle, Washington, 98195. dabaker@u.washington.edu.|Howard Hughes Medical Institute, University of Washington, Seattle, Washington, 98195. dabaker@u.washington.edu.
authors: David
authors: D
authors: Baker
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data*; D003198:Computer Simulation; D030562:Databases, Protein; D007391:International Cooperation; D020407:Internet; D008958:Models, Molecular; D015233:Models, Statistical; D019906:Nuclear Magnetic Resonance, Biomolecular; D000072756:Protein Conformation, alpha-Helical; D000072757:Protein Conformation, beta-Strand; D017510:Protein Folding; D054730:Protein Interaction Domains and Motifs; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D011506:Proteins
keywords: CASP11; NMR; Rosetta; contact assisted; protein structure prediction