Publications

Featured Papers

• Computational design of generalist cyclopropanases with stereodivergent selectivity
  Shen Z, Siriboe MG, Ren X, Dayananda T, Jenkins JL, Khare SD, Fasan R. Nature Communications (2026).
• Constrained Diffusion for Protein Design with Hard Structural Constraints
  Christopher JK, Seamann A, Cui J, Khare SD, Fioretto F. Proceedings of ICLR 2026 (preprint: bioRxiv, 2025).
• Graph attention with structural features improves the generalizability of identifying functional sequences at a protein interface
  Ash J, Francino-Urdaniz IM, Kells SP, Davis CN, Whitehead TA, Khare SD. bioRxiv (2025).
• Massively parallel, computationally guided design of a proenzyme
  Yachnin BJ, Azouz LR, White RE III, Minetti CASA, et al., Khare SD. Proc. Natl. Acad. Sci. USA 119:e2116097119 (2022).
• Stimulus-responsive self-assembly of protein-based fractals by computational design
  Hernández NE, Hansen WA, Zhu D, Shea ME, et al., Khare SD. Nature Chemistry 11:605–614 (2019).
• Data-driven supervised learning of a viral protease specificity landscape from deep sequencing and molecular simulations
  Pethe MA, Rubenstein AB, Khare SD. Proc. Natl. Acad. Sci. USA 116:168–176 (2019).
• Computational Design of a Photocontrolled Cytosine Deaminase
  Blacklock KM, Yachnin BJ, Woolley GA, Khare SD. J. Am. Chem. Soc. 140:14–17 (2018).

All Publications

Khare lab authors are shown in bold. For the most up-to-date list, see also Google Scholar and PubMed.

2026

• Computational design of generalist cyclopropanases with stereodivergent selectivity
  Shen Z, Siriboe MG, Ren X, Dayananda T, Jenkins JL, Khare SD, Fasan R. Nature Communications (2026).
• Constrained Diffusion for Protein Design with Hard Structural Constraints
  Christopher JK, Seamann A, Cui J, Khare SD, Fioretto F. Proceedings of ICLR 2026 (preprint: bioRxiv, 2025).

2025

• Graph attention with structural features improves the generalizability of identifying functional sequences at a protein interface
  Ash J, Francino-Urdaniz IM, Kells SP, Davis CN, Whitehead TA, Khare SD. bioRxiv (2025).
• Protease-Catalyzed Synthesis of Water-Soluble Oligohistidine
  Black SP, Liu M, Xia K, Khare SD, Gross RA. Industrial Biotechnology (New Rochelle, N.Y.), 3, 140–145.
• Rational Design of Stapled Covalent Peptide Modifiers of Oncoprotein E6 from Human Papillomavirus
  Emanuelson C, Naro Y, Shade O, Liu M, Khare SD, Deiters A. ACS Chemical Biology, 3, 746–757.

2024

• Synergistic Multi-Pronged Interactions Mediate the Effective Inhibition of Alpha-Synuclein Aggregation by the Chaperone HtrA1
  Chinchilla P, Wang B, Lubin JH, Yang X, Roth J, Khare SD, Baum J. bioRxiv : the preprint server for biology.

2023

• Genetic Encoding of Arylazopyrazole Phenylalanine for Optical Control of Translation
  Janosko CP, Shade O, Courtney TM, Horst TJ, Liu M, Khare SD, Deiters A. ACS Omega, 29, 26590–26596.
• Modeling of ACE2 and Antibodies Bound to SARS-CoV-2 Provides Insights into Infectivity and Immune Evasion
  Lubin JH, Markosian C, Balamurugan D, Ma MT, Chen CH, Liu D, Pasqualini R, Arap W, Burley SK, Khare SD. JCI Insight, 13.
• Multifaceted Interactions Mediated by Intrinsically Disordered Regions Play Key Roles in Alpha Synuclein Aggregation
  Khare SD, Chinchilla P, Baum J. Current Opinion in Structural Biology, 102579.
• Computational Design of Nanomolar-Binding Antibodies Specific to Multiple SARS-CoV-2 Variants
  Hernandez NE, Jankowski W, Frick R, Kelow SP, Lubin JH, Simhadri V, Adolf-Bryfogle J, Khare SD, Dunbrack RL Jr, Gray JJ, Sauna ZE. Heliyon, 4, e15032.
• A Bis(imidazole)-Based Cysteine Labeling Tool for Metalloprotein Assembly
  Ahmad R, Tyryshkin AM, Xie L, Hansen WA, Yachnin BJ, Emge TJ, Mashrai A, Khare SD, Knapp S. Journal of Inorganic Biochemistry, 112206.

2022

• Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution
  Burley SK, Berman HM, Chiu W, Dai W, Flatt JW, Hudson BP, Khare SD, et al. Biophysical Reviews (2022).
• Outcome of Crash Course Training on Protein Structure Prediction with Artificial Intelligence
  Balamurugan D, Dougherty M, Lubin JH, Arias P, Chan J, et al., Khare SD. bioRxiv 2022.09.01.506222 (2022). [preprint]
• Computational Design of Photochromic Proteins
  Dolan EM, Khare SD. In Molecular Photoswitches, Wiley (2022). [book chapter]
• Introducing a New Bond-Forming Activity in an Archaeal DNA Polymerase by Structure-Guided Mutagenesis
  Aggarwal T, Hansen WA, Hong J, Ganguly A, York DM, et al., Khare SD. ACS Chemical Biology (2022).
• Tuning Enzyme Thermostability via Computationally Guided Covalent Stapling and Structural Analysis
  Iannuzzelli JA, Bacik JP, Moore EJ, Shen Z, Irving EM, Khare SD, Fasan R. Biochemistry (2022).
• Genetic and Structural Analysis of SARS-CoV-2 Spike Protein for Universal Epitope Selection
  Markosian C, Staquicini DI, Dogra P, Dodero-Rojas E, et al., Khare SD. Mol. Biol. Evol. 39:msac091 (2022).
• Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first 6 months of the COVID-19 pandemic
  Lubin JH, Zardecki C, Dolan EM, Lu C, Shen Z, Dutta S, ..., Khare SD, Burley SK. Proteins: Struct. Funct. Bioinfo. 90:1054–1080 (2022).
• Massively parallel, computationally guided design of a proenzyme
  Yachnin BJ, Azouz LR, White RE III, Minetti CASA, et al., Khare SD. Proc. Natl. Acad. Sci. USA 119:e2116097119 (2022).
• Enantioselective Synthesis of α-Trifluoromethyl Amines via Biocatalytic N–H Bond Insertion
  Nam D, Tinoco A, Shen Z, Adukure RD, Sreenilayam G, Khare SD, Fasan R. J. Am. Chem. Soc. (2022).
• Highly stereoselective and enantiodivergent synthesis of cyclopropylphosphonates with engineered carbene transferases
  Ren X, Chandgude AL, Carminati DM, Shen Z, Khare SD, Fasan R. Chemical Science (2022).

2021

• Biomolecular Condensates: Sequence Determinants of Phase Separation, Microstructural Organization, Enzymatic Activity, and Material Properties
  Schuster BS, Regy RM, Dolan EM, Ranganath AK, Jovic N, Khare SD, Shi Z, Mittal J. J. Phys. Chem. B (2021).
• Computational structure prediction provides a plausible mechanism for electron transfer by the outer membrane protein Cyc2 from Acidithiobacillus ferrooxidans
  Jiang V, Khare SD, Banta S. Protein Science (2021).

2020

• Virtual Boot Camp: COVID-19 evolution and structural biology
  Burley SK, Bromberg Y, Craig P, Duffy S, Dutta S, Hall BL, Hudson BP, Jiang J, Khare SD, Koeppe JR, Lubin JH, Mills SA, Pikaart MJ, Roberts R, Sarma V, Singh J, Tischfield JA, Xie L, Zardecki C. Biochem. Mol. Biol. Educ. 48:511–513 (2020).
• Recent progress in designing protein-based supramolecular assemblies
  Hansen WA, Khare SD. Curr. Opin. Struct. Biol. 63:106–114 (2020).
• Macromolecular modeling and design in Rosetta: recent methods and frameworks
  Leman JK, Weitzner BD, Lewis SM, ..., Khare SD, ..., Bonneau R. Nat. Methods 17:665–680 (2020).
• Protease-catalyzed l-aspartate oligomerization: substrate selectivity and computational modeling
  Yang F, Totsingan F, Dolan E, Khare SD, Gross RA. ACS Omega 5:4403–4414 (2020).
• Mathematical Models of Protease-Based Enzymatic Biosensors
  Agrawal DK, Dolan EM, Hernandez NE, Blacklock KM, Khare SD, Sontag ED. ACS Synth. Biol. 9:198–208 (2020).

2019

• Stimulus-responsive self-assembly of protein-based fractals by computational design
  Hernández NE, Hansen WA, Zhu D, Shea ME, et al., Khare SD. Nat. Chem. 11:605–614 (2019).
• Photoswitchable Affinity Reagents: Computational Design and Efficient Red-Light Switching
  Yasuike N, Blacklock KM, Lu H, Jaikaran ASI, McDonald S, Uppalapati M, Khare SD, Woolley GA. ChemPhotoChem (2019).
• Data-driven supervised learning of a viral protease specificity landscape from deep sequencing and molecular simulations
  Pethe MA, Rubenstein AB, Khare SD. Proc. Natl. Acad. Sci. USA 116:168–176 (2019).

2018

• Systematic comparison of Amber and Rosetta energy functions for protein structure evaluation
  Rubenstein AB, Blacklock KM, Nguyen H, Case DA, Khare SD. J. Chem. Theor. Comput. 14:6015–6025 (2018).
• Multi-Pronged Interactions Underlie Inhibition of α-Synuclein Aggregation by β-Synuclein
  Williams JK, Yang X, Atieh TB, Olson MP, Khare SD, Baum J. J. Mol. Biol. 430:2360–2371 (2018).
• A computational method for the design of nested proteins using loop-directed domain insertion
  Blacklock KM, Yang L, Mulligan VK, Khare SD. Proteins: Struct. Funct. Bioinfo. 86:354–369 (2018).
• Computational Assessment of Thioether Isosteres
  Barrows RD, Blacklock KM, Rablen PR, Khare SD, Knapp S. J. Mol. Graph. Model. 80:282–292 (2018).
• Computational Design of a Photocontrolled Cytosine Deaminase
  Blacklock KM, Yachnin BJ, Woolley GA, Khare SD. J. Am. Chem. Soc. 140:14–17 (2018).

2017

• Enzyme stabilization via computationally guided protein stapling
  Moore EJ, Zorine D, Hansen WA, Khare SD, Fasan R. Proc. Natl. Acad. Sci. USA 114:12472–12477 (2017).
• Computational design of a stimulus responsive multi-enzyme supramolecular assembly
  Yang L, Dolan EM, Tan SK, Lin T, Sontag ED, Khare SD. ChemBioChem 18:2000–2006 (2017).
• Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition
  Davis KM, Schramma KR, Hansen WA, Bacik JP, Khare SD, Seyedsayamdost MR, Ando N. Proc. Natl. Acad. Sci. USA 114:10420–10425 (2017).
• Formation of fibrils by beta-synuclein at mildly acidic pH mediated by charged interaction clusters
  Moriarty GM, Olson MP, Atieh T, Janowska M, Khare SD, Baum J. J. Biol. Chem. 292:16368–16379 (2017).
• Design and Evolution of a Macrocyclic Peptide Inhibitor of the Sonic Hedgehog/Patched Interaction
  Owens AE, de Paola I, Hansen WA, Liu Y-W, Khare SD, Fasan R. J. Am. Chem. Soc. 139:12559–12568 (2017).
• MFPred: Rapid and accurate prediction of multispecificity at protein-peptide interfaces using self-consistent mean-field theory
  Rubenstein AB, Pethe MA, Khare SD. PLoS Comput. Biol. 13:e1005614 (2017).
• Benchmarking a protein design method for introducing multinuclear metal ion-binding sites at oligomeric protein interfaces
  Hansen WA, Khare SD. Protein Sci. 26:1584–1594 (2017).
• Designing a circularly permuted carboxypeptidase G2 enzyme for an autoinhibited enzyme drug
  Yachnin BJ, Khare SD. Protein Eng. Des. Sel. 30:321–331 (2017).
• Large-scale structure-based prediction and identification of novel protease substrates using computational protein design
  Pethe MA, Rubenstein AB, Khare SD. J. Mol. Biol. 429:220–236 (2017).
• Computational design of ligand binding proteins
  Tinberg CE, Khare SD. Methods Mol. Biol. 1529:363–373 (2017).

2016

• Improving Binding Affinity and Selectivity of Computationally Designed Ligand-Binding Proteins Using Experiments
  Tinberg CE, Khare SD. Methods Mol. Biol. 1414:155–171 (2016).
• Computational design of metalloproteins using unnatural amino acids
  Hansen WA, Mills JH, Khare SD. Methods Mol. Biol. 1414:173–185 (2016).

2015

• Introduction to the Rosetta Special Collection
  Khare SD, Whitehead TA. PLoS One 10:e0144326 (2015).
• FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants
  Bednar D, Beerens K, Sebestova E, Bendl J, Khare SD, Chaloupkova R, Prokop Z, Brezovsky J, Baker D, Damborsky J. PLoS Comput. Biol. 11:e1004556 (2015).
• Structural principles for computational and de novo design of 4Fe-4S metalloproteins
  Nanda V, Senn S, Pike DH, Rodriguez-Granillo A, Hansen WA, Khare SD, Noy D. Biochim. Biophys. Acta 1857:201–207 (2015).
• CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge
  Smith RD, Damm-Ganamet KL, Dunbar JB Jr, Ahmed A, Chinnaswamy K, Delproposto JE, Kubish GM, Tinberg CE, Khare SD, Dou J, Doyle L, Stuckey JA, Baker D, Carlson HA. J. Chem. Inf. Model. 56:1022–1031 (2015).

2014

• Computational redesign of metalloenzymes for introducing new activities
  Greisen PJ Jr, Khare SD. Methods Mol. Biol. 1216:265–273 (2014).

2013

• Emerging themes in the computational design of novel enzymes and protein-protein interfaces
  Khare SD, Fleishman SJ. FEBS Lett. 587:1147–1154 (2013).
• Computational Design of an Unnatural Amino Acid Dependent Metalloprotein with Atomic Level Accuracy
  Mills JH, Khare SD, Bolduc JM, Forouhar F, Mulligan VK, Lew S, Seetharaman J, Tong L, Stoddard BL, Baker D. J. Am. Chem. Soc. 135:13393–13399 (2013).
• Computational Design of Ligand Binding Proteins with High Affinity and Selectivity
  Tinberg CE, Khare SD, Dou J, Doyle L, Nelson J, Schena A, Jankowski W, Kalodimos CG, Johnsson K, Stoddard BL, Baker D. Nature 501:212–216 (2013). (Tinberg and Khare contributed equally.)
• Engineering V-type nerve agents detoxifying enzymes using computationally focused libraries
  Cherny I, Greisen PJ, Ashani Y, Khare SD, Oberdorfer G, Leader H, Baker D, Tawfik DS. ACS Chem. Biol. 8:2394–2403 (2013).

2012

• Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis
  Khare SD, Kipnis Y, Greisen PJ, Takeuchi R, Ashani Y, Goldsmith M, Song Y, Gallaher JL, Silman I, Leader H, Sussman JL, Stoddard BL, Tawfik DS, Baker D. Nat. Chem. Biol. 8:294–300 (2012).
• Computational Design of Catalytic Dyads and Oxyanion Holes for Ester Hydrolysis
  Richter F, Blomberg R, Khare SD, Kiss G, Kuzin AP, Smith AJ, Gallaher JL, Pianowski Z, Helgeson RC, Grjasnow A, Xiao R, Seetharaman J, Su M, Vorobiev S, Lew S, Forouhar F, Kornhaber GJ, Hunt JF, Montelione GT, Tong L, Houk KN, Hilvert D, Baker D. J. Am. Chem. Soc. 134:16197–16207 (2012).