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For: Thyme SB, Song Y, Brunette TJ, Szeto MD, Kusak L, Bradley P, Baker D. Massively parallel determination and modeling of endonuclease substrate specificity. Nucleic Acids Res 2014;42:13839-52. [PMID: 25389263 PMCID: PMC4267613 DOI: 10.1093/nar/gku1096] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open

For:	Thyme SB, Song Y, Brunette TJ, Szeto MD, Kusak L, Bradley P, Baker D. Massively parallel determination and modeling of endonuclease substrate specificity. Nucleic Acids Res 2014;42:13839-52. [PMID: 25389263 PMCID: PMC4267613 DOI: 10.1093/nar/gku1096] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open

Number

Cited by Other Article(s)

Nawimanage R, Yuan Z, Casares M, Joshi R, Lohman JR, Gimble FS. Structure-function studies of two yeast homing endonucleases that evolved to cleave identical targets with dissimilar rates and specificities. J Mol Biol 2022;434:167550. [DOI: 10.1016/j.jmb.2022.167550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 10/18/2022]

Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, Bradley P, Bystroff C, Conway P, Cooper S, Correia BE, Coventry B, Das R, De Jong RM, DiMaio F, Dsilva L, Dunbrack R, Ford AS, Frenz B, Fu DY, Geniesse C, Goldschmidt L, Gowthaman R, Gray JJ, Gront D, Guffy S, Horowitz S, Huang PS, Huber T, Jacobs TM, Jeliazkov JR, Johnson DK, Kappel K, Karanicolas J, Khakzad H, Khar KR, Khare SD, Khatib F, Khramushin A, King IC, Kleffner R, Koepnick B, Kortemme T, Kuenze G, Kuhlman B, Kuroda D, Labonte JW, Lai JK, Lapidoth G, Leaver-Fay A, Lindert S, Linsky T, London N, Lubin JH, Lyskov S, Maguire J, Malmström L, Marcos E, Marcu O, Marze NA, Meiler J, Moretti R, Mulligan VK, Nerli S, Norn C, Ó'Conchúir S, Ollikainen N, Ovchinnikov S, Pacella MS, Pan X, Park H, Pavlovicz RE, Pethe M, Pierce BG, Pilla KB, Raveh B, Renfrew PD, Burman SSR, Rubenstein A, Sauer MF, Scheck A, Schief W, Schueler-Furman O, Sedan Y, Sevy AM, Sgourakis NG, Shi L, Siegel JB, Silva DA, Smith S, Song Y, Stein A, Szegedy M, Teets FD, Thyme SB, Wang RYR, Watkins A, Zimmerman L, Bonneau R. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nat Methods 2020;17:665-680. [PMID: 32483333 PMCID: PMC7603796 DOI: 10.1038/s41592-020-0848-2] [Citation(s) in RCA: 417] [Impact Index Per Article: 104.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 04/22/2020] [Indexed: 12/12/2022]

Affiliation(s)

Julia Koehler Leman Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA. Department of Biology, New York University, New York, New York, USA.
Brian D Weitzner Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA Department of Biochemistry, University of Washington, Seattle, WA, USA Institute for Protein Design, University of Washington, Seattle, WA, USA Lyell Immunopharma Inc., Seattle, WA, USA
Steven M Lewis Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA Department of Biochemistry, Duke University, Durham, NC, USA Cyrus Biotechnology, Seattle, WA, USA
Jared Adolf-Bryfogle Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
Nawsad Alam Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
Rebecca F Alford Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
Melanie Aprahamian Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA
David Baker Department of Biochemistry, University of Washington, Seattle, WA, USA Institute for Protein Design, University of Washington, Seattle, WA, USA
Kyle A Barlow Graduate Program in Bioinformatics, University of California San Francisco, San Francisco, CA, USA
Patrick Barth Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland Baylor College of Medicine, Department of Pharmacology, Houston, TX, USA
Benjamin Basanta Department of Biochemistry, University of Washington, Seattle, WA, USA Biological Physics Structure and Design PhD Program, University of Washington, Seattle, WA, USA
Brian J Bender Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
Kristin Blacklock Institute of Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
Jaume Bonet Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland
Scott E Boyken Institute for Protein Design, University of Washington, Seattle, WA, USA Lyell Immunopharma Inc., Seattle, WA, USA
Phil Bradley Fred Hutchinson Cancer Research Center, Seattle, WA, USA
Chris Bystroff Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA
Patrick Conway Department of Biochemistry, University of Washington, Seattle, WA, USA
Seth Cooper Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
Bruno E Correia Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland
Brian Coventry Department of Biochemistry, University of Washington, Seattle, WA, USA
Rhiju Das Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
René M De Jong DSM Biotechnology Center, Delft, the Netherlands
Frank DiMaio Department of Biochemistry, University of Washington, Seattle, WA, USA Institute for Protein Design, University of Washington, Seattle, WA, USA
Lorna Dsilva Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
Roland Dunbrack Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA
Alexander S Ford Department of Biochemistry, University of Washington, Seattle, WA, USA
Brandon Frenz Institute for Protein Design, University of Washington, Seattle, WA, USA Cyrus Biotechnology, Seattle, WA, USA
Darwin Y Fu Department of Chemistry, Vanderbilt University, Nashville, TN, USA
Caleb Geniesse Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
Lukasz Goldschmidt Department of Biochemistry, University of Washington, Seattle, WA, USA
Ragul Gowthaman University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
Jeffrey J Gray Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA
Dominik Gront Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
Sharon Guffy Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
Scott Horowitz Department of Chemistry & Biochemistry, University of Denver, Denver, CO, USA The Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
Po-Ssu Huang Department of Biochemistry, University of Washington, Seattle, WA, USA
Thomas Huber Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
Tim M Jacobs Program in Bioinformatics and Computational Biology, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
Jeliazko R Jeliazkov Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA
David K Johnson Center for Computational Biology, University of Kansas, Lawrence, KS, USA
Kalli Kappel Biophysics Program, Stanford University, Stanford, CA, USA
John Karanicolas Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA
Hamed Khakzad Swiss Institute of Bioinformatics, Lausanne, Switzerland Institute for Computational Science, University of Zurich, Zurich, Switzerland S3IT, University of Zurich, Zurich, Switzerland
Karen R Khar Cyrus Biotechnology, Seattle, WA, USA Center for Computational Biology, University of Kansas, Lawrence, KS, USA
Sagar D Khare Institute of Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA Department of Chemistry and Chemical Biology, The State University of New Jersey, Piscataway, NJ, USA Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ, USA Computational Biology and Molecular Biophysics Program, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
Firas Khatib Department of Computer and Information Science, University of Massachusetts Dartmouth, Dartmouth, MA, USA
Alisa Khramushin Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
Indigo C King Department of Biochemistry, University of Washington, Seattle, WA, USA Cyrus Biotechnology, Seattle, WA, USA
Robert Kleffner Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
Brian Koepnick Department of Biochemistry, University of Washington, Seattle, WA, USA
Tanja Kortemme Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
Georg Kuenze Department of Chemistry, Vanderbilt University, Nashville, TN, USA Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
Brian Kuhlman Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
Daisuke Kuroda Medical Device Development and Regulation Research Center, School of Engineering, University of Tokyo, Tokyo, Japan Department of Bioengineering, School of Engineering, University of Tokyo, Tokyo, Japan
Jason W Labonte Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA Department of Chemistry, Franklin & Marshall College, Lancaster, PA, USA
Jason K Lai Baylor College of Medicine, Department of Pharmacology, Houston, TX, USA
Gideon Lapidoth Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
Andrew Leaver-Fay Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
Steffen Lindert Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA
Thomas Linsky Department of Biochemistry, University of Washington, Seattle, WA, USA Institute for Protein Design, University of Washington, Seattle, WA, USA
Nir London Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
Joseph H Lubin Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
Sergey Lyskov Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
Jack Maguire Program in Bioinformatics and Computational Biology, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
Lars Malmström Swiss Institute of Bioinformatics, Lausanne, Switzerland Institute for Computational Science, University of Zurich, Zurich, Switzerland S3IT, University of Zurich, Zurich, Switzerland Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
Enrique Marcos Department of Biochemistry, University of Washington, Seattle, WA, USA Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain
Orly Marcu Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
Nicholas A Marze Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
Jens Meiler Center for Structural Biology, Vanderbilt University, Nashville, TN, USA Departments of Chemistry, Pharmacology and Biomedical Informatics, Vanderbilt University, Nashville, TN, USA Institute for Chemical Biology, Vanderbilt University, Nashville, TN, USA
Rocco Moretti Department of Chemistry, Vanderbilt University, Nashville, TN, USA
Vikram Khipple Mulligan Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA Department of Biochemistry, University of Washington, Seattle, WA, USA Institute for Protein Design, University of Washington, Seattle, WA, USA
Santrupti Nerli Department of Computer Science, University of California Santa Cruz, Santa Cruz, CA, USA
Christoffer Norn Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
Shane Ó'Conchúir Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
Noah Ollikainen Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
Sergey Ovchinnikov Department of Biochemistry, University of Washington, Seattle, WA, USA Institute for Protein Design, University of Washington, Seattle, WA, USA Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
Michael S Pacella Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
Xingjie Pan Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
Hahnbeom Park Department of Biochemistry, University of Washington, Seattle, WA, USA
Ryan E Pavlovicz Department of Biochemistry, University of Washington, Seattle, WA, USA Institute for Protein Design, University of Washington, Seattle, WA, USA Cyrus Biotechnology, Seattle, WA, USA
Manasi Pethe Department of Chemistry and Chemical Biology, The State University of New Jersey, Piscataway, NJ, USA Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
Brian G Pierce University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
Kala Bharath Pilla Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
Barak Raveh Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
P Douglas Renfrew Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
Shourya S Roy Burman Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
Aliza Rubenstein Institute of Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA Computational Biology and Molecular Biophysics Program, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
Marion F Sauer Chemical and Physical Biology Program, Vanderbilt Vaccine Center, Vanderbilt University, Nashville, TN, USA
Andreas Scheck Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland
William Schief Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
Ora Schueler-Furman Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
Yuval Sedan Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
Alexander M Sevy Chemical and Physical Biology Program, Vanderbilt Vaccine Center, Vanderbilt University, Nashville, TN, USA
Nikolaos G Sgourakis Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
Lei Shi Department of Biochemistry, University of Washington, Seattle, WA, USA Institute for Protein Design, University of Washington, Seattle, WA, USA
Justin B Siegel Department of Chemistry, University of California, Davis, Davis, CA, USA Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California, USA Genome Center, University of California, Davis, Davis, CA, USA
Daniel-Adriano Silva Department of Biochemistry, University of Washington, Seattle, WA, USA
Shannon Smith Department of Chemistry, Vanderbilt University, Nashville, TN, USA
Yifan Song Department of Biochemistry, University of Washington, Seattle, WA, USA Institute for Protein Design, University of Washington, Seattle, WA, USA Cyrus Biotechnology, Seattle, WA, USA
Amelie Stein Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
Maria Szegedy Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
Frank D Teets Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
Summer B Thyme Department of Biochemistry, University of Washington, Seattle, WA, USA
Ray Yu-Ruei Wang Department of Biochemistry, University of Washington, Seattle, WA, USA
Andrew Watkins Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
Lior Zimmerman Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
Richard Bonneau Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA. Department of Biology, New York University, New York, New York, USA. Department of Computer Science, New York University, New York, NY, USA. Center for Data Science, New York University, New York, NY, USA.

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Laforet M, McMurrough TA, Vu M, Brown CM, Zhang K, Junop MS, Gloor GB, Edgell DR. Modifying a covarying protein-DNA interaction changes substrate preference of a site-specific endonuclease. Nucleic Acids Res 2019;47:10830-10841. [PMID: 31602462 PMCID: PMC6847045 DOI: 10.1093/nar/gkz866] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/17/2019] [Accepted: 10/09/2019] [Indexed: 12/23/2022] Open

Wrenbeck EE, Faber MS, Whitehead TA. Deep sequencing methods for protein engineering and design. Curr Opin Struct Biol 2017;45:36-44. [PMID: 27886568 PMCID: PMC5440218 DOI: 10.1016/j.sbi.2016.11.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 11/01/2016] [Indexed: 11/27/2022]

Hauser K, Essuman B, He Y, Coutsias E, Garcia-Diaz M, Simmerling C. A human transcription factor in search mode. Nucleic Acids Res 2015;44:63-74. [PMID: 26673724 PMCID: PMC4705650 DOI: 10.1093/nar/gkv1091] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 10/07/2015] [Indexed: 12/14/2022] Open

SMRT Sequencing for Parallel Analysis of Multiple Targets and Accurate SNP Phasing. G3-GENES GENOMES GENETICS 2015;5:2801-8. [PMID: 26497143 PMCID: PMC4683651 DOI: 10.1534/g3.115.023317] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]