Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites.

Autor: Hosseinzadeh P; University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA.; Knight Campus Center, University of Oregon, Eugene, OR, USA., Watson PR; Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA., Craven TW; University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA., Li X; University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA., Rettie S; University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA.; Molecular and Cellular Biology Ph.D. Program, University of Washington, Seattle, WA, USA., Pardo-Avila F; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA., Bera AK; University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA., Mulligan VK; University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA.; Systems Biology, Center for Computational Biology, Flatiron Institute, New York, NY, USA., Lu P; University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA.; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China., Ford AS; University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA., Weitzner BD; University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA.; Lyell Immunopharma, Inc., Seattle, WA, USA., Stewart LJ; University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA., Moyer AP; University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA.; Molecular Engineering Ph.D. Program, University of Washington, Seattle, WA, USA., Di Piazza M; University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA., Whalen JG; University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA., Greisen PJ; University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA.; Novo Nordisk A/S, Måløv, Denmark., Christianson DW; Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA., Baker D; University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA. dabaker@uw.edu.

Publikováno v: Nature communications [Nat Commun] 2021 Jun 07; Vol. 12 (1), pp. 3384. Date of Electronic Publication: 2021 Jun 07.

Macromolecular modeling and design in Rosetta: recent methods and frameworks.

Autor: Leman JK; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA. Julia.koehler.leman@nyu.edu.; Department of Biology, New York University, New York, New York, USA. Julia.koehler.leman@nyu.edu., Weitzner BD; 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., Lewis SM; 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., Adolf-Bryfogle J; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA., Alam N; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel., Alford RF; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA., Aprahamian M; Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA., Baker D; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Barlow KA; Graduate Program in Bioinformatics, University of California San Francisco, San Francisco, CA, USA., Barth P; Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.; Baylor College of Medicine, Department of Pharmacology, Houston, TX, USA., Basanta B; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Biological Physics Structure and Design PhD Program, University of Washington, Seattle, WA, USA., Bender BJ; Department of Pharmacology, Vanderbilt University, Nashville, TN, USA., Blacklock K; Institute of Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA., Bonet J; Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland., Boyken SE; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Lyell Immunopharma Inc., Seattle, WA, USA., Bradley P; Fred Hutchinson Cancer Research Center, Seattle, WA, USA., Bystroff C; Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA., Conway P; Department of Biochemistry, University of Washington, Seattle, WA, USA., Cooper S; Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA., Correia BE; Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland., Coventry B; Department of Biochemistry, University of Washington, Seattle, WA, USA., Das R; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA., De Jong RM; DSM Biotechnology Center, Delft, the Netherlands., DiMaio F; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Dsilva L; Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA., Dunbrack R; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA., Ford AS; Department of Biochemistry, University of Washington, Seattle, WA, USA., Frenz B; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Cyrus Biotechnology, Seattle, WA, USA., Fu DY; Department of Chemistry, Vanderbilt University, Nashville, TN, USA., Geniesse C; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA., Goldschmidt L; Department of Biochemistry, University of Washington, Seattle, WA, USA., Gowthaman R; 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., Gray JJ; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.; Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA., Gront D; Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland., Guffy S; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA., Horowitz S; Department of Chemistry & Biochemistry, University of Denver, Denver, CO, USA.; The Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA., Huang PS; Department of Biochemistry, University of Washington, Seattle, WA, USA., Huber T; Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia., Jacobs TM; Program in Bioinformatics and Computational Biology, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA., Jeliazkov JR; Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA., Johnson DK; Center for Computational Biology, University of Kansas, Lawrence, KS, USA., Kappel K; Biophysics Program, Stanford University, Stanford, CA, USA., Karanicolas J; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA., Khakzad H; Swiss Institute of Bioinformatics, Lausanne, Switzerland.; Institute for Computational Science, University of Zurich, Zurich, Switzerland.; S3IT, University of Zurich, Zurich, Switzerland., Khar KR; Cyrus Biotechnology, Seattle, WA, USA.; Center for Computational Biology, University of Kansas, Lawrence, KS, USA., Khare SD; 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., Khatib F; Department of Computer and Information Science, University of Massachusetts Dartmouth, Dartmouth, MA, USA., Khramushin A; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel., King IC; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Cyrus Biotechnology, Seattle, WA, USA., Kleffner R; Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA., Koepnick B; Department of Biochemistry, University of Washington, Seattle, WA, USA., Kortemme T; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA., Kuenze G; Department of Chemistry, Vanderbilt University, Nashville, TN, USA.; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA., Kuhlman B; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA., Kuroda D; 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., Labonte JW; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.; Department of Chemistry, Franklin & Marshall College, Lancaster, PA, USA., Lai JK; Baylor College of Medicine, Department of Pharmacology, Houston, TX, USA., Lapidoth G; Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel., Leaver-Fay A; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA., Lindert S; Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA., Linsky T; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., London N; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel., Lubin JH; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA., Lyskov S; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA., Maguire J; Program in Bioinformatics and Computational Biology, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA., Malmström L; 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., Marcos E; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain., Marcu O; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel., Marze NA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA., Meiler J; 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., Moretti R; Department of Chemistry, Vanderbilt University, Nashville, TN, USA., Mulligan VK; 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., Nerli S; Department of Computer Science, University of California Santa Cruz, Santa Cruz, CA, USA., Norn C; Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel., Ó'Conchúir S; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA., Ollikainen N; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA., Ovchinnikov S; 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., Pacella MS; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA., Pan X; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA., Park H; Department of Biochemistry, University of Washington, Seattle, WA, USA., Pavlovicz RE; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Cyrus Biotechnology, Seattle, WA, USA., Pethe M; 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., Pierce BG; 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., Pilla KB; Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia., Raveh B; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel., Renfrew PD; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA., Burman SSR; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA., Rubenstein A; 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., Sauer MF; Chemical and Physical Biology Program, Vanderbilt Vaccine Center, Vanderbilt University, Nashville, TN, USA., Scheck A; Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland., Schief W; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA., Schueler-Furman O; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel., Sedan Y; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel., Sevy AM; Chemical and Physical Biology Program, Vanderbilt Vaccine Center, Vanderbilt University, Nashville, TN, USA., Sgourakis NG; Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA., Shi L; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Siegel JB; 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., Silva DA; Department of Biochemistry, University of Washington, Seattle, WA, USA., Smith S; Department of Chemistry, Vanderbilt University, Nashville, TN, USA., Song Y; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Cyrus Biotechnology, Seattle, WA, USA., Stein A; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA., Szegedy M; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA., Teets FD; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA., Thyme SB; Department of Biochemistry, University of Washington, Seattle, WA, USA., Wang RY; Department of Biochemistry, University of Washington, Seattle, WA, USA., Watkins A; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA., Zimmerman L; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel., Bonneau R; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA. Bonneau@nyu.edu.; Department of Biology, New York University, New York, New York, USA. Bonneau@nyu.edu.; Department of Computer Science, New York University, New York, NY, USA. Bonneau@nyu.edu.; Center for Data Science, New York University, New York, NY, USA. Bonneau@nyu.edu.

Publikováno v: Nature methods [Nat Methods] 2020 Jul; Vol. 17 (7), pp. 665-680. Date of Electronic Publication: 2020 Jun 01.

Integration of the Rosetta suite with the python software stack via reproducible packaging and core programming interfaces for distributed simulation.

Autor: Ford AS; Institute for Protein Innovation, Boston, Massachusetts.; Institute for Protein Design, University of Washington, Seattle, Washington.; Department of Biochemistry, University of Washington, Seattle, Washington., Weitzner BD; Institute for Protein Design, University of Washington, Seattle, Washington.; Department of Biochemistry, University of Washington, Seattle, Washington.; Lyell Immunopharma, Inc., Seattle, Washington., Bahl CD; Institute for Protein Innovation, Boston, Massachusetts.; Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.; Department of Pediatrics, Harvard Medical School, Boston, Massachusetts.

Publikováno v: Protein science : a publication of the Protein Society [Protein Sci] 2020 Jan; Vol. 29 (1), pp. 43-51. Date of Electronic Publication: 2019 Dec 02.

De novo design of potent and selective mimics of IL-2 and IL-15.

Autor: Silva DA; Institute for Protein Design, University of Washington, Seattle, WA, USA. dadriano@uw.edu.; Department of Biochemistry, University of Washington, Seattle, WA, USA. dadriano@uw.edu., Yu S; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Department of Bioengineering, University of Washington, Seattle, WA, USA., Ulge UY; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Department of Bioengineering, University of Washington, Seattle, WA, USA., Spangler JB; Departments of Biomedical Engineering and Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.; Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA, USA., Jude KM; Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA, USA., Labão-Almeida C; Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal., Ali LR; Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA., Quijano-Rubio A; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Department of Bioengineering, University of Washington, Seattle, WA, USA., Ruterbusch M; Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA., Leung I; Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA, USA., Biary T; Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA., Crowley SJ; Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA., Marcos E; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain., Walkey CD; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Department of Biochemistry, University of Washington, Seattle, WA, USA., Weitzner BD; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Department of Biochemistry, University of Washington, Seattle, WA, USA., Pardo-Avila F; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA., Castellanos J; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Department of Biochemistry, University of Washington, Seattle, WA, USA., Carter L; Institute for Protein Design, University of Washington, Seattle, WA, USA., Stewart L; Institute for Protein Design, University of Washington, Seattle, WA, USA., Riddell SR; Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA, USA., Pepper M; Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA., Bernardes GJL; Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.; Department of Chemistry, University of Cambridge, Cambridge, UK., Dougan M; Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA., Garcia KC; Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA, USA. kcgarcia@stanford.edu.; Howard Hughes Medical Institute, Chevy Chase, MD, USA. kcgarcia@stanford.edu., Baker D; Institute for Protein Design, University of Washington, Seattle, WA, USA. dabaker@uw.edu.; Department of Biochemistry, University of Washington, Seattle, WA, USA. dabaker@uw.edu.; Howard Hughes Medical Institute, Chevy Chase, MD, USA. dabaker@uw.edu.

Publikováno v: Nature [Nature] 2019 Jan; Vol. 565 (7738), pp. 186-191. Date of Electronic Publication: 2019 Jan 09.

I am a United Academic Worker.

Autor: Weitzner BD; Brian D. Weitzner is a postdoctoral fellow at the University of Washington in Seattle. Do you have an interesting career story? Send it to SciCareerEditor@aaas.org.

Publikováno v: Science (New York, N.Y.) [Science] 2017 Oct 13; Vol. 358 (6360), pp. 266.