Publications by authors named "Sagar D Khare"

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Highly efficient enzymes designed from scratch.
Zhuofan Shen, Sagar D Khare

Nature· July 2025

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Protease-Catalyzed Synthesis of Water-Soluble Oligohistidine.
Sarah P Black, Melinda Liu, Ke Xia, Sagar D Khare, Richard A Gross

Ind Biotechnol (New Rochelle N Y)· June 2025

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Martini 3 coarse-grained model of enzymes: Framework with validation by all-atom simulations and x-ray diffraction measurements.
Mason Hooten, N Sanjeeva Murthy, Nityananda Pal, Sagar D Khare, Adam J Gormley

J Chem Phys· April 2025

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Rational Design of Stapled Covalent Peptide Modifiers of Oncoprotein E6 from Human Papillomavirus.
Cole Emanuelson, Yuta Naro, Olivia Shade, Melinda Liu, Sagar D Khare

ACS Chem Biol· March 2025

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Synergistic Multi-Pronged Interactions Mediate the Effective Inhibition of Alpha-Synuclein Aggregation by the Chaperone HtrA1.
Priscilla Chinchilla, Baifan Wang, Joseph H Lubin, Xue Yang, Jonathan Roth, Sagar D Khare

bioRxiv· November 2024

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Prediction and design of protease enzyme specificity using a structure-aware graph convolutional network.
Changpeng Lu, Joseph H Lubin, Vidur V Sarma, Samuel Z Stentz, Guanyang Wang, Sagar D Khare

Proc Natl Acad Sci U S A· September 2023

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Corrigendum to "Computational design of nanomolar-binding antibodies specific to multiple SARS-CoV-2 variants by engineering a specificity switch of antibody 80R using RosettaAntibodyDesign (RAbD) results in potential generalizable therapeutic antibodies for novel SARS-CoV-2 virus" [Heliyon 9(4) (April 2023) e15032].
Nancy E Hernandez, Wojciech Jankowski, Rahel Frick, Simon P Kelow, Joseph H Lubin, Sagar D Khare

Heliyon· August 2023

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A Bis(imidazole)-based cysteine labeling tool for metalloprotein assembly.
Raheel Ahmad, Alexei M Tyryshkin, Lingjun Xie, William A Hansen, Brahm J Yachnin, Sagar D Khare

J Inorg Biochem· July 2023

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Modeling of ACE2 and antibodies bound to SARS-CoV-2 provides insights into infectivity and immune evasion.
Joseph H Lubin, Christopher Markosian, D Balamurugan, Minh T Ma, Chih-Hsiung Chen, Sagar D Khare

JCI Insight· July 2023

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Genetic Encoding of Arylazopyrazole Phenylalanine for Optical Control of Translation.
Chasity P Janosko, Olivia Shade, Taylor M Courtney, Trevor J Horst, Melinda Liu, Sagar D Khare

ACS Omega· July 2023

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Multifaceted interactions mediated by intrinsically disordered regions play key roles in alpha synuclein aggregation.
Sagar D Khare, Priscilla Chinchilla, Jean Baum

Curr Opin Struct Biol· June 2023

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Monomer Choice Influences -Acryloyl Amino Acid Grafter Conversion via Protease Catalysis.
Cody B Edson, Melinda Liu, Filbert Totsingan, Evan O'Berg, John Salvucci, Sagar D Khare

Biomacromolecules· April 2023

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Computational design of nanomolar-binding antibodies specific to multiple SARS-CoV-2 variants by engineering a specificity switch of antibody 80R using RosettaAntibodyDesign (RAbD) results in potential generalizable therapeutic antibodies for novel SARS-CoV-2 virus.
Nancy E Hernandez, Wojciech Jankowski, Rahel Frick, Simon P Kelow, Joseph H Lubin, Sagar D Khare

Heliyon· April 2023

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Prediction and Design of Protease Enzyme Specificity Using a Structure-Aware Graph Convolutional Network.
Changpeng Lu, Joseph H Lubin, Vidur V Sarma, Samuel Z Stentz, Guanyang Wang, Sagar D Khare

bioRxiv· February 2023

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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, Samantha G Martinusen, Christine Zardecki, Cassandra Olivas, Mickayla Bacorn, Sagar D Khare

bioRxiv· January 2023

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Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future.
Stephen K Burley, Helen M Berman, Wah Chiu, Wei Dai, Justin W Flatt, Sagar D Khare

Biophys Rev· December 2022

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Introducing a New Bond-Forming Activity in an Archaeal DNA Polymerase by Structure-Guided Enzyme Redesign.
Tushar Aggarwal, William A Hansen, Jonathan Hong, Abir Ganguly, Darrin M York, Sagar D Khare

ACS Chem Biol· July 2022

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Highly stereoselective and enantiodivergent synthesis of cyclopropylphosphonates with engineered carbene transferases.
Xinkun Ren, Ajay L Chandgude, Daniela M Carminati, Zhuofan Shen, Sagar D Khare

Chem Sci· July 2022

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Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first 6 months of the COVID-19 pandemic.
Joseph H Lubin, Christine Zardecki, Elliott M Dolan, Changpeng Lu, Zhuofan Shen, Sagar D Khare

Proteins· May 2022

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Genetic and Structural Analysis of SARS-CoV-2 Spike Protein for Universal Epitope Selection.
Christopher Markosian, Daniela I Staquicini, Prashant Dogra, Esteban Dodero-Rojas, Joseph H Lubin, Sagar D Khare

Mol Biol Evol· May 2022

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Tuning Enzyme Thermostability via Computationally Guided Covalent Stapling and Structural Basis of Enhanced Stabilization.
Jacob A Iannuzzelli, John-Paul Bacik, Eric J Moore, Zhuofan Shen, Ellen M Irving, Sagar D Khare

Biochemistry· May 2022

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Massively parallel, computationally guided design of a proenzyme.
Brahm J Yachnin, Laura R Azouz, Ralph E White, Conceição A S A Minetti, David P Remeta, Sagar D Khare

Proc Natl Acad Sci U S A· April 2022

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Enantioselective Synthesis of α-Trifluoromethyl Amines via Biocatalytic N-H Bond Insertion with Acceptor-Acceptor Carbene Donors.
Donggeon Nam, Antonio Tinoco, Zhuofan Shen, Ronald D Adukure, Gopeekrishnan Sreenilayam, Sagar D Khare

J Am Chem Soc· February 2022

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Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces.
Joseph H Lubin, Christopher Markosian, D Balamurugan, Renata Pasqualini, Wadih Arap, Sagar D Khare

bioRxiv· December 2021

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Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks.
Julia Koehler Leman, Sergey Lyskov, Steven M Lewis, Jared Adolf-Bryfogle, Rebecca F Alford, Sagar D Khare

Nat Commun· November 2021

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