Sagar Khare

Sagar Khare

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Sagar Khare

Sagar Khare

Publications by authors named "Sagar Khare"

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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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http://dx.doi.org/10.1021/acsomega.9b03290DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7066554PMC
March 2020

Mathematical Models of Protease-Based Enzymatic Biosensors.

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

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

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http://dx.doi.org/10.1021/acssynbio.9b00279DOI Listing
February 2020

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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http://dx.doi.org/10.1073/pnas.1805256116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6320525PMC
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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http://dx.doi.org/10.1016/j.jmb.2018.05.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6100766PMC
August 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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http://dx.doi.org/10.1002/prot.25445DOI Listing
March 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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http://dx.doi.org/10.1016/j.jmgm.2018.01.018DOI Listing
March 2018

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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http://dx.doi.org/10.1007/978-1-4939-6637-0_19DOI Listing
January 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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http://dx.doi.org/10.1021/jacs.7b08709DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6830878PMC
January 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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http://dx.doi.org/10.1073/pnas.1708907114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5703291PMC
November 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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http://dx.doi.org/10.1002/cbic.201700425DOI Listing
October 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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http://dx.doi.org/10.1074/jbc.M117.780528DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5625065PMC
September 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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http://dx.doi.org/10.1021/jacs.7b06087DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753398PMC
September 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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http://dx.doi.org/10.1073/pnas.1703663114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5625900PMC
September 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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http://doi.wiley.com/10.1002/pro.3194
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http://dx.doi.org/10.1002/pro.3194DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5521545PMC
August 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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http://dx.doi.org/10.1371/journal.pcbi.1005614DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5507473PMC
June 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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http://dx.doi.org/10.1093/protein/gzx005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6283397PMC
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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http://dx.doi.org/10.1016/j.jmb.2016.11.031DOI Listing
January 2017

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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http://dx.doi.org/10.1007/978-1-4939-3569-7_9DOI Listing
December 2016

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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http://dx.doi.org/10.1007/978-1-4939-3569-7_10DOI Listing
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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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0144326PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4700992PMC
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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http://dx.doi.org/10.1016/j.bbabio.2015.10.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389887PMC
May 2016

FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants.

PLoS Comput Biol 2015 Nov 3;11(11):e1004556. Epub 2015 Nov 3.

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic; Enantis, Ltd., Brno, Czech Republic.

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http://dx.doi.org/10.1371/journal.pcbi.1004556DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631455PMC
November 2015

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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http://dx.doi.org/10.1007/978-1-4939-1486-9_14DOI Listing
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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http://dx.doi.org/10.1021/cb4004892DOI Listing
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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http://dx.doi.org/10.1021/ja403503mDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3863684PMC
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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http://dx.doi.org/10.1016/j.febslet.2012.12.009DOI Listing
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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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019230PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3095599PMC
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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http://dx.doi.org/10.1002/pro.604DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3081553PMC
April 2011

Quantitative reactivity profiling predicts functional cysteines in proteomes.

Nature 2010 Dec 17;468(7325):790-5. Epub 2010 Nov 17.

The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1038/nature09472DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3058684PMC
December 2010

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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http://dx.doi.org/10.2174/138920307783018703DOI Listing
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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http://www.jbc.org/lookup/doi/10.1074/jbc.M701600200
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http://dx.doi.org/10.1074/jbc.M701600200DOI Listing
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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http://dx.doi.org/10.1080/13506120600960486DOI Listing
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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http://dx.doi.org/10.1073/pnas.0511266103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1413921PMC
February 2006

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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http://dx.doi.org/10.1002/prot.20629DOI Listing
November 2005

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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http://dx.doi.org/10.1371/journal.pcbi.0010030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1193989PMC
August 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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http://dx.doi.org/10.1016/j.str.2004.09.011DOI Listing
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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http://dx.doi.org/10.1073/pnas.0406650101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC524068PMC
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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http://linkinghub.elsevier.com/retrieve/pii/S002228360400031
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http://dx.doi.org/10.1016/j.jmb.2004.01.002DOI Listing
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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http://dx.doi.org/10.1016/j.jmb.2003.09.069DOI Listing
November 2003