Publications by authors named "Sagar D Khare"

49Publications

Virtual Boot Camp: COVID-19 evolution and structural biology.

Biochem Mol Biol Educ 2020 09 14;48(5):511-513. Epub 2020 Aug 14.

Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.

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September 2020

Recent progress in designing protein-based supramolecular assemblies.

Curr Opin Struct Biol 2020 08 20;63:106-114. Epub 2020 Jun 20.

Institute for Quantitative Biomedicine, Rutgers - The State University of New Jersey, NJ, USA; Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, NJ, USA. Electronic address:

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August 2020

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

Authors:
Julia Koehler Leman Brian D Weitzner Steven M Lewis Jared Adolf-Bryfogle Nawsad Alam Rebecca F Alford Melanie Aprahamian David Baker Kyle A Barlow Patrick Barth Benjamin Basanta Brian J Bender Kristin Blacklock Jaume Bonet Scott E Boyken Phil Bradley Chris Bystroff Patrick Conway Seth Cooper Bruno E Correia Brian Coventry Rhiju Das René M De Jong Frank DiMaio Lorna Dsilva Roland Dunbrack Alexander S Ford Brandon Frenz Darwin Y Fu Caleb Geniesse Lukasz Goldschmidt Ragul Gowthaman Jeffrey J Gray Dominik Gront Sharon Guffy Scott Horowitz Po-Ssu Huang Thomas Huber Tim M Jacobs Jeliazko R Jeliazkov David K Johnson Kalli Kappel John Karanicolas Hamed Khakzad Karen R Khar Sagar D Khare Firas Khatib Alisa Khramushin Indigo C King Robert Kleffner Brian Koepnick Tanja Kortemme Georg Kuenze Brian Kuhlman Daisuke Kuroda Jason W Labonte Jason K Lai Gideon Lapidoth Andrew Leaver-Fay Steffen Lindert Thomas Linsky Nir London Joseph H Lubin Sergey Lyskov Jack Maguire Lars Malmström Enrique Marcos Orly Marcu Nicholas A Marze Jens Meiler Rocco Moretti Vikram Khipple Mulligan Santrupti Nerli Christoffer Norn Shane Ó'Conchúir Noah Ollikainen Sergey Ovchinnikov Michael S Pacella Xingjie Pan Hahnbeom Park Ryan E Pavlovicz Manasi Pethe Brian G Pierce Kala Bharath Pilla Barak Raveh P Douglas Renfrew Shourya S Roy Burman Aliza Rubenstein Marion F Sauer Andreas Scheck William Schief Ora Schueler-Furman Yuval Sedan Alexander M Sevy Nikolaos G Sgourakis Lei Shi Justin B Siegel Daniel-Adriano Silva Shannon Smith Yifan Song Amelie Stein Maria Szegedy Frank D Teets Summer B Thyme Ray Yu-Ruei Wang Andrew Watkins Lior Zimmerman Richard Bonneau

Nat Methods 2020 07 1;17(7):665-680. Epub 2020 Jun 1.

Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA.

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July 2020

Protease-Catalyzed l-Aspartate Oligomerization: Substrate Selectivity and Computational Modeling.

ACS Omega 2020 Mar 25;5(9):4403-4414. Epub 2020 Feb 25.

Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, 1623 15th Street, Troy, New York 12180, United States.

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March 2020

Mathematical Models of Protease-Based Enzymatic Biosensors.

ACS Synth Biol 2020 02 7;9(2):198-208. Epub 2020 Feb 7.

Department of Bioengineering , Northeastern University , Boston , Massachusetts 02120 , United States.

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February 2020

Photoswitchable affinity reagents: Computational design and efficient red-light switching.

ChemPhotoChem 2019 Jun 4;3(6):431-440. Epub 2019 Mar 4.

Department of Chemistry, University of Toronto, 80 St. George St., Toronto, M5S 3H6, Canada.

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June 2019

Data-driven supervised learning of a viral protease specificity landscape from deep sequencing and molecular simulations.

Proc Natl Acad Sci U S A 2019 01 26;116(1):168-176. Epub 2018 Dec 26.

Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854;

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January 2019

Multi-Pronged Interactions Underlie Inhibition of α-Synuclein Aggregation by β-Synuclein.

J Mol Biol 2018 08 18;430(16):2360-2371. Epub 2018 May 18.

Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA. Electronic address:

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August 2018

Computational assessment of thioether isosteres.

J Mol Graph Model 2018 03 1;80:282-292. Epub 2018 Feb 1.

Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 610 Taylor Rd., Piscataway, NJ 08854 USA. Electronic address:

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March 2018

Computational Design of a Photocontrolled Cytosine Deaminase.

J Am Chem Soc 2018 01 28;140(1):14-17. Epub 2017 Dec 28.

Department of Chemistry and Chemical Biology, Center for Integrative Proteomics Research, Rutgers University , New Brunswick, New Jersey 08854, United States.

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January 2018

A computational method for the design of nested proteins by loop-directed domain insertion.

Proteins 2018 03 24;86(3):354-369. Epub 2018 Jan 24.

Institute for Quantitative Biomedicine, Rutgers The State University of New Jersey, Piscataway, New Jersey.

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March 2018

Enzyme stabilization via computationally guided protein stapling.

Proc Natl Acad Sci U S A 2017 11 6;114(47):12472-12477. Epub 2017 Nov 6.

Department of Chemistry, University of Rochester, Rochester, NY 14627;

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November 2017

Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition.

Proc Natl Acad Sci U S A 2017 09 11;114(39):10420-10425. Epub 2017 Sep 11.

Department of Chemistry, Princeton University, Princeton, NJ 08544;

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September 2017

Computation-Guided Design of a Stimulus-Responsive Multienzyme Supramolecular Assembly.

Chembiochem 2017 10 1;18(20):2000-2006. Epub 2017 Sep 1.

Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.

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October 2017

Design and Evolution of a Macrocyclic Peptide Inhibitor of the Sonic Hedgehog/Patched Interaction.

J Am Chem Soc 2017 09 30;139(36):12559-12568. Epub 2017 Aug 30.

Department of Chemistry, University of Rochester , 120 Trustee Road, Rochester, New York 14627, United States.

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September 2017

A pH-dependent switch promotes β-synuclein fibril formation via glutamate residues.

J Biol Chem 2017 09 14;292(39):16368-16379. Epub 2017 Jul 14.

From the Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854

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September 2017

MFPred: Rapid and accurate prediction of protein-peptide recognition multispecificity using self-consistent mean field theory.

PLoS Comput Biol 2017 Jun 26;13(6):e1005614. Epub 2017 Jun 26.

Computational Biology & Molecular Biophysics Program, Rutgers, The State University of New Jersey, Piscataway, NJ.

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June 2017

Benchmarking a computational design method for the incorporation of metal ion-binding sites at symmetric protein interfaces.

Protein Sci 2017 Aug 31;26(8):1584-1594. Epub 2017 May 31.

Institute for Quantitative Biomedicine at Rutgers, 610 Taylor Road, Piscataway, New Jersey, 08854.

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August 2017

Engineering carboxypeptidase G2 circular permutations for the design of an autoinhibited enzyme.

Protein Eng Des Sel 2017 04;30(4):321-331

Department of Chemistry & Chemical Biology and the Center for Integrative Proteomics, Rutgers University, Piscataway, NJ 08854, USA.

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April 2017

Large-Scale Structure-Based Prediction and Identification of Novel Protease Substrates Using Computational Protein Design.

J Mol Biol 2017 01 6;429(2):220-236. Epub 2016 Dec 6.

Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Computational Biology & Molecular Biophysics Program, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA. Electronic address:

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January 2017

Computational Design of Ligand Binding Proteins.

Methods Mol Biol 2017 ;1529:363-373

Department of Chemistry and Chemical Biology, Center for Integrative Proteomics Research, Institute for Quantitative Biomedicine at Rutgers, Rutgers The State University of New Jersey, Piscataway, NJ, 08854, USA.

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January 2018

Computational Design of Multinuclear Metalloproteins Using Unnatural Amino Acids.

Methods Mol Biol 2016 ;1414:173-85

Center for Integrative Proteomics Research, Rutgers State University of New Jersey, Piscataway, NJ, 08854, USA.

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December 2016

Improving Binding Affinity and Selectivity of Computationally Designed Ligand-Binding Proteins Using Experiments.

Methods Mol Biol 2016 ;1414:155-71

Department of Chemistry and Chemical Biology, Rutgers State University of New Jersey, Piscataway, NJ, 08854, USA.

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December 2016

Introduction to the Rosetta Special Collection.

PLoS One 2015 29;10(12):e0144326. Epub 2015 Dec 29.

Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, United States of America.

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July 2016

Structural principles for computational and de novo design of 4Fe-4S metalloproteins.

Biochim Biophys Acta 2016 May 9;1857(5):531-538. Epub 2015 Oct 9.

Bioenergetics and Protein Design Laboratory, Migal - Galilee Research Institute, South Industrial Zone, Kiryat Shmona 11016, Israel.

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May 2016

Computational redesign of metalloenzymes for catalyzing new reactions.

Methods Mol Biol 2014 ;1216:265-73

Department of Biochemistry, University of Washington, Seattle, WA, USA.

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May 2015

Engineering V-type nerve agents detoxifying enzymes using computationally focused libraries.

ACS Chem Biol 2013 Nov 4;8(11):2394-403. Epub 2013 Oct 4.

Department of Biological Chemistry, Weizmann Institute of Science , Rehovot 76100, Israel.

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November 2013

Computational design of an unnatural amino acid dependent metalloprotein with atomic level accuracy.

J Am Chem Soc 2013 Sep 29;135(36):13393-9. Epub 2013 Aug 29.

Department of Biochemistry and ⊥Biomolecular Structure and Design Program, University of Washington , Seattle, Washington, United States.

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September 2013

Emerging themes in the computational design of novel enzymes and protein-protein interfaces.

FEBS Lett 2013 Apr 19;587(8):1147-54. Epub 2012 Dec 19.

Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.

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April 2013

De novo enzyme design using Rosetta3.

PLoS One 2011 16;6(5):e19230. Epub 2011 May 16.

Department of Biochemistry, University of Washington, Seattle, Washington, United States of America.

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October 2011

Restricted sidechain plasticity in the structures of native proteins and complexes.

Protein Sci 2011 Apr;20(4):753-7

Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.

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April 2011

Molecular mechanisms of polypeptide aggregation in human diseases.

Curr Protein Pept Sci 2007 Dec;8(6):573-9

Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, NC 27599, USA.

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December 2007

The length dependence of the polyQ-mediated protein aggregation.

J Biol Chem 2007 Aug 25;282(35):25487-92. Epub 2007 Jun 25.

Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA.

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August 2007

FALS mutations in Cu, Zn superoxide dismutase destabilize the dimer and increase dimer dissociation propensity: a large-scale thermodynamic analysis.

Amyloid 2006 Dec;13(4):226-35

Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC 27599, USA.

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December 2006

Common dynamical signatures of familial amyotrophic lateral sclerosis-associated structurally diverse Cu, Zn superoxide dismutase mutants.

Proc Natl Acad Sci U S A 2006 Feb 17;103(9):3147-52. Epub 2006 Feb 17.

Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, 27599, USA.

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February 2006

Molecular origin of polyglutamine aggregation in neurodegenerative diseases.

PLoS Comput Biol 2005 Aug 26;1(3):230-5. Epub 2005 Aug 26.

Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA.

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August 2005

Sequence and structural determinants of Cu, Zn superoxide dismutase aggregation.

Proteins 2005 Nov;61(3):617-32

Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.

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November 2005

New insights into FAK signaling and localization based on detection of a FAT domain folding intermediate.

Structure 2004 Dec;12(12):2161-71

Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

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December 2004

The rate and equilibrium constants for a multistep reaction sequence for the aggregation of superoxide dismutase in amyotrophic lateral sclerosis.

Proc Natl Acad Sci U S A 2004 Oct 8;101(42):15094-9. Epub 2004 Oct 8.

Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA.

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October 2004

Can contact potentials reliably predict stability of proteins?

J Mol Biol 2004 Mar;336(5):1223-38

Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

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March 2004

Folding of Cu, Zn superoxide dismutase and familial amyotrophic lateral sclerosis.

J Mol Biol 2003 Nov;334(3):515-25

Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC 27599, USA.

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November 2003