Publications by authors named "Sagar D Khare"

49Publications

Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first six months of the COVID-19 pandemic.

Authors:
Joseph H Lubin Christine Zardecki Elliott M Dolan Changpeng Lu Zhuofan Shen Shuchismita Dutta John D Westbrook Brian P Hudson David S Goodsell Jonathan K Williams Maria Voigt Vidur Sarma Lingjun Xie Thejasvi Venkatachalam Steven Arnold Luz Helena Alfaro Alvarado Kevin Catalfano Aaliyah Khan Erika McCarthy Sophia Staggers Brea Tinsley Alan Trudeau Jitendra Singh Lindsey Whitmore Helen Zheng Matthew Benedek Jenna Currier Mark Dresel Ashish Duvvuru Britney Dyszel Emily Fingar Elizabeth M Hennen Michael Kirsch Ali A Khan Charlotte Labrie-Cleary Stephanie Laporte Evan Lenkeit Kailey Martin Marilyn Orellana Melanie Ortiz-Alvarez de la Campa Isaac Paredes Baleigh Wheeler Allison Rupert Andrew Sam Katherine See Santiago Soto Zapata Paul A Craig Bonnie L Hall Jennifer Jiang Julia R Koeppe Stephen A Mills Michael J Pikaart Rebecca Roberts Yana Bromberg J Steen Hoyer Siobain Duffy Jay Tischfield Francesc X Ruiz Eddy Arnold Jean Baum Jesse Sandberg Grace Brannigan Sagar D Khare Stephen K Burley

bioRxiv 2020 Dec 4. Epub 2020 Dec 4.

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December 2020

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

Authors:
Stephen K Burley Yana Bromberg Paul Craig Siobain Duffy Shuchismita Dutta Bonnie L Hall Brian P Hudson Jennifer Jiang Sagar D Khare Julia R Koeppe Joseph H Lubin Stephen A Mills Michael J Pikaart Rebecca Roberts Vidur Sarma Jitendra Singh Jay A Tischfield Lingjun Xie Christine Zardecki

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.

Authors:
William A Hansen Sagar D Khare

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.

Authors:
Fan Yang Filbert Totsingan Elliott Dolan Sagar D Khare Richard A Gross

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.

Authors:
Deepak K Agrawal Elliott M Dolan Nancy E Hernandez Kristin M Blacklock Sagar D Khare Eduardo D Sontag

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

Stimulus-responsive self-assembly of protein-based fractals by computational design.

Authors:
Nancy E Hernández William A Hansen Denzel Zhu Maria E Shea Marium Khalid Viacheslav Manichev Matthew Putnins Muyuan Chen Anthony G Dodge Lu Yang Ileana Marrero-Berríos Melissa Banal Phillip Rechani Torgny Gustafsson Leonard C Feldman Sang-Hyuk Lee Lawrence P Wackett Wei Dai Sagar D Khare

Nat Chem 2019 07 17;11(7):605-614. Epub 2019 Jun 17.

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

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July 2019

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

Authors:
Nobuo Yasuike Kristin M Blacklock Huixin Lu Anna S I Jaikaran Sherin McDonald Maruti Uppalapati Sagar D Khare G Andrew Woolley

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.

Authors:
Manasi A Pethe Aliza B Rubenstein Sagar D Khare

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

Systematic Comparison of Amber and Rosetta Energy Functions for Protein Structure Evaluation.

Authors:
Aliza B Rubenstein Kristin Blacklock Hai Nguyen David A Case Sagar D Khare

J Chem Theory Comput 2018 Nov 12;14(11):6015-6025. Epub 2018 Oct 12.

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November 2018

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

Authors:
Jonathan K Williams Xue Yang Tamr B Atieh Michael P Olson Sagar D Khare Jean Baum

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.

Authors:
Robert D Barrows Kristin M Blacklock Paul R Rablen Sagar D Khare Spencer Knapp

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.

Authors:
Kristin M Blacklock Brahm J Yachnin G Andrew Woolley Sagar D Khare

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.

Authors:
Kristin M Blacklock Lu Yang Vikram K Mulligan Sagar D Khare

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.

Authors:
Eric J Moore Dmitri Zorine William A Hansen Sagar D Khare Rudi Fasan

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.

Authors:
Katherine M Davis Kelsey R Schramma William A Hansen John P Bacik Sagar D Khare Mohammad R Seyedsayamdost Nozomi Ando

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.

Authors:
Lu Yang Elliott M Dolan Sophia K Tan Tianyun Lin Eduardo D Sontag Sagar D Khare

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.

Authors:
Andrew E Owens Ivan de Paola William A Hansen Yi-Wen Liu Sagar D Khare Rudi Fasan

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.

Authors:
Gina M Moriarty Michael P Olson Tamr B Atieh Maria K Janowska Sagar D Khare Jean Baum

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.

Authors:
Aliza B Rubenstein Manasi A Pethe Sagar D Khare

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.

Authors:
William A Hansen Sagar D Khare

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.

Authors:
Brahm J Yachnin Sagar D Khare

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.

Authors:
Manasi A Pethe Aliza B Rubenstein Sagar D Khare

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.

Authors:
Christine E Tinberg Sagar D Khare

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.

Authors:
William A Hansen Jeremy H Mills Sagar D Khare

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.

Authors:
Christine E Tinberg Sagar D Khare

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.

Authors:
Sagar D Khare Timothy A Whitehead

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.

Authors:
Vikas Nanda Stefan Senn Douglas H Pike Agustina Rodriguez-Granillo Will A Hansen Sagar D Khare Dror Noy

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

CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge.

Authors:
Richard D Smith Kelly L Damm-Ganamet James B Dunbar Aqeel Ahmed Krishnapriya Chinnaswamy James E Delproposto Ginger M Kubish Christine E Tinberg Sagar D Khare Jiayi Dou Lindsey Doyle Jeanne A Stuckey David Baker Heather A Carlson

J Chem Inf Model 2016 06 9;56(6):1022-31. Epub 2015 Oct 9.

Department of Medicinal Chemistry, University of Michigan , 428 Church Street, Ann Arbor, Michigan 48109-1065, United States.

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June 2016

Computational redesign of metalloenzymes for catalyzing new reactions.

Authors:
Per Greisen Sagar D Khare

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.

Authors:
Izhack Cherny Per Greisen Yacov Ashani Sagar D Khare Gustav Oberdorfer Haim Leader David Baker Dan S Tawfik

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 ligand-binding proteins with high affinity and selectivity.

Authors:
Christine E Tinberg Sagar D Khare Jiayi Dou Lindsey Doyle Jorgen W Nelson Alberto Schena Wojciech Jankowski Charalampos G Kalodimos Kai Johnsson Barry L Stoddard David Baker

Nature 2013 Sep 4;501(7466):212-216. Epub 2013 Sep 4.

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

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September 2013

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

Authors:
Jeremy H Mills Sagar D Khare Jill M Bolduc Farhad Forouhar Vikram Khipple Mulligan Scott Lew Jayaraman Seetharaman Liang Tong Barry L Stoddard David Baker

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.

Authors:
Sagar D Khare Sarel J Fleishman

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

Computational design of catalytic dyads and oxyanion holes for ester hydrolysis.

Authors:
Florian Richter Rebecca Blomberg Sagar D Khare Gert Kiss Alexandre P Kuzin Adam J T Smith Jasmine Gallaher Zbigniew Pianowski Roger C Helgeson Alexej Grjasnow Rong Xiao Jayaraman Seetharaman Min Su Sergey Vorobiev Scott Lew Farhad Forouhar Gregory J Kornhaber John F Hunt Gaetano T Montelione Liang Tong K N Houk Donald Hilvert David Baker

J Am Chem Soc 2012 Oct 21;134(39):16197-206. Epub 2012 Sep 21.

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

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October 2012

Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis.

Authors:
Sagar D Khare Yakov Kipnis Per Greisen Ryo Takeuchi Yacov Ashani Moshe Goldsmith Yifan Song Jasmine L Gallaher Israel Silman Haim Leader Joel L Sussman Barry L Stoddard Dan S Tawfik David Baker

Nat Chem Biol 2012 Feb 5;8(3):294-300. Epub 2012 Feb 5.

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

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February 2012

RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite.

Authors:
Sarel J Fleishman Andrew Leaver-Fay Jacob E Corn Eva-Maria Strauch Sagar D Khare Nobuyasu Koga Justin Ashworth Paul Murphy Florian Richter Gordon Lemmon Jens Meiler David Baker

PLoS One 2011 24;6(6):e20161. Epub 2011 Jun 24.

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

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November 2011

De novo enzyme design using Rosetta3.

Authors:
Florian Richter Andrew Leaver-Fay Sagar D Khare Sinisa Bjelic David Baker

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.

Authors:
Sarel J Fleishman Sagar D Khare Nobuyasu Koga David Baker

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.

Authors:
Sagar D Khare Nikolay V Dokholyan

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.

Authors:
Sunjay Barton Ron Jacak Sagar D Khare Feng Ding Nikolay V Dokholyan

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.

Authors:
Sagar D Khare Michael Caplow Nikolay V Dokholyan

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.

Authors:
Sagar D Khare Nikolay V Dokholyan

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.

Authors:
Sagar D Khare Feng Ding Kenneth N Gwanmesia Nikolay V Dokholyan

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.

Authors:
Sagar D Khare Kyle C Wilcox Peng Gong Nikolay V Dokholyan

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.

Authors:
Richard D S Dixon Yiwen Chen Feng Ding Sagar D Khare Kirk C Prutzman Michael D Schaller Sharon L Campbell Nikolay V Dokholyan

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.

Authors:
Sagar D Khare Michael Caplow Nikolay V Dokholyan

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?

Authors:
Jainab Khatun Sagar D Khare Nikolay V Dokholyan

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.

Authors:
Sagar D Khare Feng Ding Nikolay V Dokholyan

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