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RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design 1 1¤a 1,2 3 4 Po-Ssu Huang , Yih-En Andrew Ban , Florian Richter , Ingemar Andre , Robert Vernon , William R. 1 ¤b 1,5 Schief * , David Baker * 1 Department of Biochemistry, University of Washington, Seattle, Washington, United States of America, 2 Interdisciplinary Program in Biomolecular Structure and Design, University of Washington, Seattle, Washington, United States of America, 3 Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden, 4 Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada, 5 Howard Hughes Medical Institute, University of Washington, Seattle, Washington, United States of America Abstract We describe RosettaRemodel, a generalized framework for flexible protein design that provides a versatile and convenient interface to the Rosetta modeling suite. RosettaRemodel employs a unified interface, called a blueprint, which allows detailed control over many aspects of flexible backbone protein design calculations. RosettaRemodel allows the construction and elaboration of customized protocols for a wide range of design problems ranging from loop insertion and deletion, disulfide engineering, domain assembly, loop remodeling, motif grafting, symmetrical units, to de novo structure modeling. Citation: Huang P-S, Ban Y-EA, Richter F, Andre I, Vernon R, et al. (2011) RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design. PLoS ONE 6(8): e24109. doi:10.1371/journal.pone.0024109 Editor: V