For Publishers
DiscoveryMetadataPeer reviewHostingPublishing
For Researchers
JoinPublishReviewCollect
Register
Blog
About
Search
Advanced search
My ScienceOpen
Search
For Publishers
For Researchers
Blog
About
68
views
51
references
 Top references
cited by
153
    
0 reviews
 Review
0
comments
 Comment
0
recommends
+1 Recommend
0 collections
    0
    shares
      261
      similar
       All similar
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design

      research-article

      Read this article at

      ScienceOpenPublisherPMC
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          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.

          Related collections

          Most cited references51

          • Record: found
          • Abstract: not found
          • Article: not found

          Protein structure prediction using Rosetta.

          Carol A Rohl, Charlie E M Strauss, Kira Misura … (2004)
          Article 0 comments Cited 412 times – based on 0 reviews     Review now
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            Kemp elimination catalysts by computational enzyme design.

            Daniela Röthlisberger, Olga Khersonsky, Andrew Wollacott … (2008)
            The design of new enzymes for reactions not catalysed by naturally occurring biocatalysts is a challenge for protein engineering and is a critical test of our understanding of enzyme catalysis. Here we describe the computational design of eight enzymes that use two different catalytic motifs to catalyse the Kemp elimination-a model reaction for proton transfer from carbon-with measured rate enhancements of up to 10(5) and multiple turnovers. Mutational analysis confirms that catalysis depends on the computationally designed active sites, and a high-resolution crystal structure suggests that the designs have close to atomic accuracy. Application of in vitro evolution to enhance the computational designs produced a >200-fold increase in k(cat)/K(m) (k(cat)/K(m) of 2,600 M(-1)s(-1) and k(cat)/k(uncat) of >10(6)). These results demonstrate the power of combining computational protein design with directed evolution for creating new enzymes, and we anticipate the creation of a wide range of useful new catalysts in the future.
            Article 0 comments Cited 292 times – based on 0 reviews     Review now
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              De novo computational design of retro-aldol enzymes.

              Lin Jiang, Eric A. Althoff, Fernando R. Clemente … (2008)
              The creation of enzymes capable of catalyzing any desired chemical reaction is a grand challenge for computational protein design. Using new algorithms that rely on hashing techniques to construct active sites for multistep reactions, we designed retro-aldolases that use four different catalytic motifs to catalyze the breaking of a carbon-carbon bond in a nonnatural substrate. Of the 72 designs that were experimentally characterized, 32, spanning a range of protein folds, had detectable retro-aldolase activity. Designs that used an explicit water molecule to mediate proton shuffling were significantly more successful, with rate accelerations of up to four orders of magnitude and multiple turnovers, than those involving charged side-chain networks. The atomic accuracy of the design process was confirmed by the x-ray crystal structure of active designs embedded in two protein scaffolds, both of which were nearly superimposable on the design model.
              Article 0 comments Cited 263 times – based on 0 reviews     Review now
                Bookmark
                All references

                Author and article information

                Contributors
                : Role: Editor
                Journal
                Journal ID (nlm-ta): PLoS One
                Journal ID (publisher-id): plos
                Journal ID (pmc): plosone
                Title: PLoS ONE
                Publisher: Public Library of Science (San Francisco, USA )
                ISSN (Electronic): 1932-6203
                Publication date Collection: 2011
                Publication date (Electronic): 31 August 2011
                Volume: 6
                Issue: 8
                Electronic Location Identifier: e24109
                Affiliations
                [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
                University of South Florida College of Medicine, United States of America
                Author notes

                Conceived and designed the experiments: P-SH YAB WRS DB. Contributed reagents/materials/analysis tools: FR IA RV. Wrote the paper: P-SH YAB WRS DB.

                [¤a]

                Current address: Arzeda Corporation, Seattle, Washington, United States of America

                [¤b]

                Current address: IAVI Neutralizing Antibody Center and Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, California, United States of America

                Article
                Publisher ID: PONE-D-11-09414
                DOI: 10.1371/journal.pone.0024109
                PMC ID: 3166072
                PubMed ID: 21909381
                SO-VID: a395b748-6538-4057-9c10-0197419a523d
                Copyright © Huang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
                History
                Date received : 16 May 2011
                Date accepted : 29 July 2011
                Page count
                Pages: 8
                Categories
                Subject: Research Article
                Subject: Biology
                Subject: Biochemistry
                Subject: Proteins
                Subject: Protein Structure
                Subject: Computational Biology
                Subject: Macromolecular Structure Analysis
                Subject: Protein Structure
                Subject: Proteomics
                Subject: Protein Engineering

                ScienceOpen disciplines: Uncategorized
                Data availability:
                ScienceOpen disciplines: Uncategorized

                Comments

                Comment on this article

                scite_

                Similar content261

                See all similar

                Cited by152

                See all cited by

                Most referenced authors978

                See all reference authors