RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design
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Open Access
- 31 August 2011
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLOS ONE
- Vol. 6 (8), e24109
- https://doi.org/10.1371/journal.pone.0024109
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.This publication has 43 references indexed in Scilit:
- Computational Design of the Sequence and Structure of a Protein-Binding PeptideJournal of the American Chemical Society, 2011
- Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder ReactionScience, 2010
- Computational Design of Calmodulin Mutants with up to 900-Fold Increase in Binding SpecificityJournal of Molecular Biology, 2009
- Macromolecular Modeling with RosettaAnnual Review of Biochemistry, 2008
- High-resolution design of a protein loopProceedings of the National Academy of Sciences of the United States of America, 2007
- Protein–Protein Docking with Backbone FlexibilityJournal of Molecular Biology, 2007
- High-resolution structure prediction and the crystallographic phase problemNature, 2007
- Full-sequence Computational Design and Solution Structure of a Thermostable Protein VariantJournal of Molecular Biology, 2007
- Computational De Novo Design and Characterization of a Four-Helix Bundle Protein that Selectively Binds a Nonbiological CofactorJournal of the American Chemical Society, 2005
- Cyclic coordinate descent: A robotics algorithm for protein loop closureProtein Science, 2003