S. Khare

发表

Molecular Dynamics Simulation of Amyloid β Dimer Formation

H. Stanley, S. Buldyrev, B. Urbanc, 2004, physics/0403040.

Restricted sidechain plasticity in the structures of native proteins and complexes

D. Baker, S. Khare, S. Fleishman, 2011, Protein science : a publication of the Protein Society.

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

Nikolay V Dokholyan, Sagar D Khare, S. Khare, 2006, Proceedings of the National Academy of Sciences of the United States of America.

Enzyme stabilization via computationally guided protein stapling

Sagar D. Khare, Eric J. Moore, Rudi Fasan, 2017, Proceedings of the National Academy of Sciences.

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

Liang Tong, Gaetano T Montelione, Donald Hilvert, 2012, Journal of the American Chemical Society.

The Length Dependence of the PolyQ-mediated Protein Aggregation*

Feng Ding, Nikolay V Dokholyan, Ron Jacak, 2007, Journal of Biological Chemistry.

Sequence and structural determinants of Cu, Zn superoxide dismutase aggregation

S. Khare, N. Dokholyan, K. Wilcox, 2005, Proteins.

Molecular mechanisms of polypeptide aggregation in human diseases.

S. Khare, N. Dokholyan, 2007, Current protein & peptide science.

De Novo Enzyme Design Using Rosetta3

David Baker, Andrew Leaver-Fay, Sagar D. Khare, 2011, PloS one.

Can contact potentials reliably predict stability of proteins?

Nikolay V Dokholyan, Jainab Khatun, Sagar D Khare, 2004, Journal of molecular biology.

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

L. Feldman, S. Khare, L. Wackett, 2019, Nature Chemistry.

Stimulus-responsive Self-Assembly of Enzymatic Fractals by Computational Design

L. Feldman, S. Khare, L. Wackett, 2018, bioRxiv.

Biophysical Mechanisms of Protein Aggregation

S. Khare, 2006 .

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

S. Khare, J. Bacik, W. A. Hansen, 2017, Proceedings of the National Academy of Sciences.

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

S. Khare, B. Yachnin, 2017, Protein engineering, design & selection : PEDS.

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

S. Khare, J. Baum, G. M. Moriarty, 2017, The Journal of Biological Chemistry.

Introducing a New Bond-Forming Activity in an Archaeal DNA Polymerase by Structure-Guided Enzyme Redesign

D. York, S. Khare, W. A. Hansen, 2021, bioRxiv.

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

S. Khare, Agustina Rodriguez-Granillo, Vikas Nanda, 2016, Biochimica et biophysica acta.

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

Joseph H. Lubin, Jonathan K. Williams, Bonnie L. Hall, 2020, bioRxiv.

Computational assessment of thioether isosteres.

S. Khare, Kristin M Blacklock, S. Knapp, 2018, Journal of molecular graphics & modelling.

Tuning Enzyme Thermostability via Computationally Guided Covalent Stapling and Structural Basis of Enhanced Stabilization

S. Khare, J. Bacik, R. Fasan, 2022, Biochemistry.

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

Jonathan K. Williams, S. Khare, J. Baum, 2018, Journal of molecular biology.

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

S. Khare, W. A. Hansen, 2017, Protein science : a publication of the Protein Society.

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

Aliza B. Rubenstein, D. Case, S. Khare, 2018, Journal of chemical theory and computation.

Genetic and Structural Analysis of SARS-CoV-2 Spike Protein for Universal Epitope Selection

Joseph H. Lubin, Vinícius G. Contessoto, J. Onuchic, 2022, Molecular biology and evolution.

Outcome of Crash Course Training on Protein Structure Prediction with Artificial Intelligence

Joseph H. Lubin, J. B. von Oehsen, S. Burley, 2022, bioRxiv.

Molecular Dynamics Simulation of Amyloid β Dimer Formation

H. Stanley, S. Buldyrev, B. Urbanc, 2004, physics/0403040.

Molecular dynamics simulation of amyloid beta dimer formation.

H. Stanley, S. Buldyrev, B. Urbanc, 2004, Biophysical journal.

Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future

A. Sali, H. Berman, J. Westbrook, 2022, Biophysical Reviews.

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

Sagar D. Khare, Aliza B. Rubenstein, Manasi A. Pethe, 2018, Proceedings of the National Academy of Sciences.

Biophysical determinants of mutational robustness in a viral molecular fitness landscape

Manasi A. Pethe, S. Khare, Dmitri Zorine, 2017, bioRxiv.

Large‐scale Structure‐based Prediction and Identification of Novel Protease Substrates using Computational Protein Design

Sagar D Khare, Manasi A. Pethe, Aliza B Rubenstein, 2016, Journal of molecular biology.

Highly stereoselective and enantiodivergent synthesis of cyclopropylphosphonates with engineered carbene transferases

S. Khare, R. Fasan, D. Carminati, 2022, Chemical science.

Quantitative reactivity profiling predicts functional cysteines in proteomes

David Baker, Benjamin F. Cravatt, Sagar Khare, 2010, Nature.

Computational Structure Prediction Provides a Plausible Mechanism for Electron Transfer by the Outer Membrane Protein Cyc2 from Acidithiobacillus ferrooxidans

S. Khare, S. Banta, Virginia Jiang, 2021, bioRxiv.

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

Dan S. Tawfik, D. Baker, Y. Ashani, 2013, ACS chemical biology.

Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis.

Ryo Takeuchi, David Baker, Joel L Sussman, 2012, Nature chemical biology.

Enantioselective Synthesis of α-Trifluoromethyl Amines via Biocatalytic N–H Bond Insertion with Acceptor-Acceptor Carbene Donors

S. Khare, R. Fasan, Zhu‐Qing Shen, 2022, Journal of the American Chemical Society.

Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces

Joseph H. Lubin, S. Burley, S. Khare, 2021, bioRxiv.

Computational design of ligand-binding proteins with high affinity and selectivity

David Baker, Barry L. Stoddard, Sagar D. Khare, 2013, Nature.

Prediction and Design of Protease Enzyme Specificity Using a Structure-Aware Graph Convolutional Network

Joseph H. Lubin, S. Khare, Sijian Wang, 2023, bioRxiv.

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

F. Ding, S. Khare, N. Dokholyan, 2004, Structure.

RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite

Jens Meiler, Florian Richter, Sarel J. Fleishman, 2011, PloS one.

Molecular Origin of Polyglutamine Aggregation in Neurodegenerative Diseases

Feng Ding, Nikolay V. Dokholyan, Sagar D. Khare, 2005, PLoS Comput. Biol..

Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future

A. Sali, H. Berman, J. Westbrook, 2022, Biophysical Reviews.

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Brian D. Weitzner, Lars Malmström, Karen R. Khar, 2020, Nature Methods.

Evolution of the SARS‐CoV‐2 proteome in three dimensions (3D) during the first 6 months of the COVID‐19 pandemic

Joseph H. Lubin, Jonathan K. Williams, Bonnie L. Hall, 2021, Proteins.

A comprehensive survey of coronaviral main protease active site diversity in 3D: Identifying and analyzing drug discovery targets in search of broad specificity inhibitors for the next coronavirus pandemic

Joseph H. Lubin, S. Burley, S. Khare, 2023, bioRxiv.

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

Lu Yang, Kristin M Blacklock, Vikram K Mulligan, 2018, Proteins.

Massively parallel, computationally guided design of a proenzyme

S. Khare, Laura R. Azouz, J. Drake, 2022, bioRxiv.

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

David Baker, Jaroslav Bendl, Jan Brezovsky, 2015, PLoS Comput. Biol..

Biomolecular Condensates: Sequence Determinants of Phase Separation, Microstructural Organization, Enzymatic Activity, and Material Properties.

S. Khare, J. Mittal, Benjamin S. Schuster, 2021, The journal of physical chemistry. B.

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

S. Khare, R. Fasan, W. A. Hansen, 2017, Journal of the American Chemical Society.

MHCEpitopeEnergy, a Flexible Rosetta-Based Biotherapeutic Deimmunization Platform

Chris Bailey-Kellogg, Vikram Khipple Mulligan, Sagar D. Khare, 2021, J. Chem. Inf. Model..

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

Sagar D. Khare, Aliza B. Rubenstein, Manasi A. Pethe, 2017, PLoS Comput. Biol..

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

Richard D. Smith, Heather A. Carlson, David Baker, 2016, J. Chem. Inf. Model..

Structure prediction for CASP7 targets using extensive all‐atom refinement with Rosetta@home

Lars Malmström, David Baker, Dylan Chivian, 2007, Proteins.

Computation‐Guided Design of a Stimulus‐Responsive Multienzyme Supramolecular Assembly

Eduardo D Sontag, Sagar D Khare, Eduardo Sontag, 2017, Chembiochem : a European journal of chemical biology.

Computational Design of Ligand Binding Proteins.

Sagar D Khare, Christine E Tinberg, S. Khare, 2017, Methods in molecular biology.

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

Nikolay V Dokholyan, Michael Caplow, Sagar D Khare, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Multifaceted interactions mediated by intrinsically disordered regions play key roles in alpha synuclein aggregation.

S. Khare, J. Baum, Priscilla Chinchilla, 2023, Current opinion in structural biology.

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

Nikolay V Dokholyan, Michael Caplow, Sagar D Khare, 2006, Amyloid : the international journal of experimental and clinical investigation : the official journal of the International Society of Amyloidosis.

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

S. Khare, R. Gross, Elliott M Dolan, 2020, ACS omega.

A Bis(imidazole)-based cysteine labeling tool for metalloprotein assembly.

S. Khare, T. Emge, W. A. Hansen, 2023, Journal of inorganic biochemistry.

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

S. Khare, Kristin M Blacklock, M. Uppalapati, 2019, ChemPhotoChem.

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

Liang Tong, Vikram Khipple Mulligan, Barry L. Stoddard, 2013, Journal of the American Chemical Society.

Ju n 20 03 1 Folding of Cu , Zn superoxide dismutase and Familial Amyotrophic Lateral Sclerosis

F. Ding, S. Khare, N. Dokholyan, 2008 .

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

Feng Ding, Nikolay V Dokholyan, Sagar D Khare, 2003, Journal of molecular biology.

Recent progress in designing protein-based supramolecular assemblies.

Sagar D Khare, William A Hansen, S. Khare, 2020, Current opinion in structural biology.

Resonant Converters Resonant Converter Theory Figure 1: High-level Resonant Converter Block Diagram An1336 Dc/dc Llc Reference Design Using the Dspic ® Dsc

S. Khare, A. Bersani, A. Dumais, 2022 .

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

S. Khare, C. Tinberg, 2016, Methods in molecular biology.

Molecular Dynamics Simulation of Amyloid b Dimer Formation

H. Stanley, S. Buldyrev, B. Urbanc, 2004 .

Modeling of ACE2 and antibodies bound to SARS-CoV-2 provides insights into infectivity and immune evasion

Joseph H. Lubin, S. Burley, S. Khare, 2023, JCI insight.

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

Sarel J Fleishman, Sagar D Khare, S. Khare, 2013, FEBS letters.

Computational redesign of metalloenzymes for catalyzing new reactions.

S. Khare, P. Greisen, 2014, Methods in molecular biology.

Monomer Choice Influences N-Acryloyl Amino Acid Grafter Conversion via Protease Catalysis.

S. Khare, R. Gross, J. Salvucci, 2023, Biomacromolecules.

Mathematical models of protease-based enzymatic biosensors

Eduardo D. Sontag, Deepak K. Agrawal, Sagar D. Khare, 2019, bioRxiv.

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Brian D. Weitzner, Karen R. Khar, Roland L. Dunbrack, 2020, Nature Methods.

Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

Jason W. Labonte, Jeffrey J. Gray, Johanna K. S. Tiemann, 2021, Nature Communications.

Computational Design of Multinuclear Metalloproteins Using Unnatural Amino Acids.

S. Khare, W. A. Hansen, J. Mills, 2016, Methods in molecular biology.

Introduction to the Rosetta Special Collection

Sagar D. Khare, Timothy A. Whitehead, S. Khare, 2015, PloS one.

Structure prediction for CASP7 targets using extensive all‐atom refinement with Rosetta@home

Andrew M Wollacott, David E. Kim, Chu Wang, 2007, Proteins.

Genetic Encoding of Arylazopyrazole Phenylalanine for Optical Control of Translation

S. Khare, A. Deiters, T. Courtney, 2023, ACS omega.