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Sagar Khare, Ph.D. - Publications

Affiliations: 
2006 University of North Carolina, Chapel Hill, Chapel Hill, NC 
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48 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Lu C, Lubin JH, Sarma VV, Stentz SZ, Wang G, Wang S, Khare SD. Prediction and design of protease enzyme specificity using a structure-aware graph convolutional network. Proceedings of the National Academy of Sciences of the United States of America. 120: e2303590120. PMID 37729196 DOI: 10.1073/pnas.2303590120  0.358
2023 Hernandez NE, Jankowski W, Frick R, Kelow SP, Lubin JH, Simhadri V, Adolf-Bryfogle J, Khare SD, Dunbrack RL, Gray JJ, Sauna ZE. 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]. Heliyon. 9: e17901. PMID 37701412 DOI: 10.1016/j.heliyon.2023.e17901  0.716
2023 Hernandez NE, Jankowski W, Frick R, Kelow SP, Lubin JH, Simhadri V, Adolf-Bryfogle J, Khare SD, Dunbrack RL, Gray JJ, Sauna ZE. 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: e15032. PMID 37035348 DOI: 10.1016/j.heliyon.2023.e15032  0.741
2023 Ahmad R, Tyryshkin AM, Xie L, Hansen WA, Yachnin BJ, Emge TJ, Mashrai A, Khare SD, Knapp S. A Bis(imidazole)-based cysteine labeling tool for metalloprotein assembly. Journal of Inorganic Biochemistry. 244: 112206. PMID 37030124 DOI: 10.1016/j.jinorgbio.2023.112206  0.726
2023 Lu C, Lubin JH, Sarma VV, Stentz SZ, Wang G, Wang S, Khare SD. Prediction and Design of Protease Enzyme Specificity Using a Structure-Aware Graph Convolutional Network. Biorxiv : the Preprint Server For Biology. PMID 36824945 DOI: 10.1101/2023.02.16.528728  0.356
2022 Aggarwal T, Hansen WA, Hong J, Ganguly A, York DM, Khare SD, Izgu EC. Introducing a New Bond-Forming Activity in an Archaeal DNA Polymerase by Structure-Guided Enzyme Redesign. Acs Chemical Biology. PMID 35776893 DOI: 10.1021/acschembio.2c00373  0.735
2021 Koehler Leman J, Lyskov S, Lewis SM, Adolf-Bryfogle J, Alford RF, Barlow K, Ben-Aharon Z, Farrell D, Fell J, Hansen WA, Harmalkar A, Jeliazkov J, Kuenze G, Krys JD, Ljubetič A, ... ... Khare SD, et al. Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks. Nature Communications. 12: 6947. PMID 34845212 DOI: 10.1038/s41467-021-27222-7  0.754
2021 Yachnin BJ, Mulligan VK, Khare SD, Bailey-Kellogg C. MHCEpitopeEnergy, a Flexible Rosetta-Based Biotherapeutic Deimmunization Platform. Journal of Chemical Information and Modeling. PMID 33900750 DOI: 10.1021/acs.jcim.1c00056  0.32
2020 Hansen WA, Khare SD. Recent progress in designing protein-based supramolecular assemblies. Current Opinion in Structural Biology. 63: 106-114. PMID 32569994 DOI: 10.1016/J.Sbi.2020.05.001  0.763
2020 Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, ... ... Khare SD, et al. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods. PMID 32483333 DOI: 10.1038/S41592-020-0848-2  0.664
2020 Agrawal DK, Dolan EM, Hernandez NE, Blacklock KM, Khare SD, Sontag ED. Mathematical Models of Protease-Based Enzymatic Biosensors. Acs Synthetic Biology. PMID 32017536 DOI: 10.1021/Acssynbio.9B00279  0.74
2019 Hernández NE, Hansen WA, Zhu D, Shea ME, Khalid M, Manichev V, Putnins M, Chen M, Dodge AG, Yang L, Marrero-Berríos I, Banal M, Rechani P, Gustafsson T, Feldman LC, ... ... Khare SD, et al. Stimulus-responsive self-assembly of protein-based fractals by computational design. Nature Chemistry. PMID 31209296 DOI: 10.1038/S41557-019-0277-Y  0.79
2019 Pethe MA, Rubenstein AB, Khare SD. Data-driven supervised learning of a viral protease specificity landscape from deep sequencing and molecular simulations. Proceedings of the National Academy of Sciences of the United States of America. 116: 168-176. PMID 30587591 DOI: 10.1073/Pnas.1805256116  0.787
2017 Moore EJ, Zorine D, Hansen WA, Khare SD, Fasan R. Enzyme stabilization via computationally guided protein stapling. Proceedings of the National Academy of Sciences of the United States of America. PMID 29109284 DOI: 10.1073/Pnas.1708907114  0.761
2017 Davis KM, Schramma KR, Hansen WA, Bacik JP, Khare SD, Seyedsayamdost MR, Ando N. Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition. Proceedings of the National Academy of Sciences of the United States of America. PMID 28893989 DOI: 10.1073/Pnas.1703663114  0.731
2017 Owens AE, de Paola I, Hansen WA, Liu YW, Khare SD, Fasan R. Design and Evolution of a Macrocyclic Peptide Inhibitor of the Sonic Hedgehog/Patched Interaction. Journal of the American Chemical Society. PMID 28759213 DOI: 10.1021/Jacs.7B06087  0.741
2017 Rubenstein AB, Pethe MA, Khare SD. MFPred: Rapid and accurate prediction of protein-peptide recognition multispecificity using self-consistent mean field theory. Plos Computational Biology. 13: e1005614. PMID 28650961 DOI: 10.1371/Journal.Pcbi.1005614  0.803
2017 Hansen WA, Khare SD. Benchmarking a computational design method for the incorporation of metal ion-binding sites at symmetric protein interfaces. Protein Science : a Publication of the Protein Society. PMID 28513090 DOI: 10.1002/Pro.3194  0.777
2017 Tinberg CE, Khare SD. Computational Design of Ligand Binding Proteins. Methods in Molecular Biology (Clifton, N.J.). 1529: 363-373. PMID 27914062 DOI: 10.1007/978-1-4939-6637-0_19  0.358
2016 Pethe MA, Rubenstein AB, Khare SD. Large-scale structure-based prediction and identification of novel protease substrates using computational protein design. Journal of Molecular Biology. PMID 27932294 DOI: 10.1016/J.Jmb.2016.11.031  0.811
2016 Hansen WA, Mills JH, Khare SD. Computational Design of Multinuclear Metalloproteins Using Unnatural Amino Acids. Methods in Molecular Biology (Clifton, N.J.). 1414: 173-85. PMID 27094291 DOI: 10.1007/978-1-4939-3569-7_10  0.799
2016 Khare SD, Rubenstein A, Pethe M. Structure-Based Prediction of Protease Multispecificity using Computational Protein Design Biophysical Journal. 110: 345a. DOI: 10.1016/J.Bpj.2015.11.1858  0.812
2015 Bednar D, Beerens K, Sebestova E, Bendl J, Khare S, Chaloupkova R, Prokop Z, Brezovsky J, Baker D, Damborsky J. FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants. Plos Computational Biology. 11: e1004556. PMID 26529612 DOI: 10.1371/Journal.Pcbi.1004556  0.497
2015 Nanda V, Senn S, Pike DH, Rodriguez-Granillo A, Hansen W, Khare SD, Noy D. Structural principles for computational and de novo design of 4Fe-4S metalloproteins. Biochimica Et Biophysica Acta. PMID 26449207 DOI: 10.1016/J.Bbabio.2015.10.001  0.753
2015 Smith RD, Damm-Ganamet KL, Dunbar JB, Ahmed A, Chinnaswamy K, Delproposto JE, Kubish GM, Tinberg CE, Khare SD, Dou J, Doyle L, Stuckey JA, Baker D, Carlson HA. CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge. Journal of Chemical Information and Modeling. PMID 26419257 DOI: 10.1021/Acs.Jcim.5B00387  0.426
2014 Greisen P, Khare SD. Computational redesign of metalloenzymes for catalyzing new reactions. Methods in Molecular Biology (Clifton, N.J.). 1216: 265-73. PMID 25213421 DOI: 10.1007/978-1-4939-1486-9_14  0.311
2013 Cherny I, Greisen P, Ashani Y, Khare SD, Oberdorfer G, Leader H, Baker D, Tawfik DS. Engineering V-type nerve agents detoxifying enzymes using computationally focused libraries. Acs Chemical Biology. 8: 2394-403. PMID 24041203 DOI: 10.1021/Cb4004892  0.345
2013 Tinberg CE, Khare SD, Dou J, Doyle L, Nelson JW, Schena A, Jankowski W, Kalodimos CG, Johnsson K, Stoddard BL, Baker D. Computational design of ligand-binding proteins with high affinity and selectivity. Nature. 501: 212-6. PMID 24005320 DOI: 10.1038/Nature12443  0.684
2013 Mills JH, Khare SD, Bolduc JM, Forouhar F, Mulligan VK, Lew S, Seetharaman J, Tong L, Stoddard BL, Baker D. Computational design of an unnatural amino acid dependent metalloprotein with atomic level accuracy. Journal of the American Chemical Society. 135: 13393-9. PMID 23924187 DOI: 10.1021/Ja403503M  0.717
2013 Khare SD, Fleishman SJ. Emerging themes in the computational design of novel enzymes and protein-protein interfaces. Febs Letters. 587: 1147-54. PMID 23262222 DOI: 10.1016/j.febslet.2012.12.009  0.381
2012 Richter F, Blomberg R, Khare SD, Kiss G, Kuzin AP, Smith AJ, Gallaher J, Pianowski Z, Helgeson RC, Grjasnow A, Xiao R, Seetharaman J, Su M, Vorobiev S, Lew S, et al. Computational design of catalytic dyads and oxyanion holes for ester hydrolysis. Journal of the American Chemical Society. 134: 16197-206. PMID 22871159 DOI: 10.1021/Ja3037367  0.592
2012 Khare SD, Kipnis Y, Greisen P, Takeuchi R, Ashani Y, Goldsmith M, Song Y, Gallaher JL, Silman I, Leader H, Sussman JL, Stoddard BL, Tawfik DS, Baker D. Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis. Nature Chemical Biology. 8: 294-300. PMID 22306579 DOI: 10.1038/Nchembio.777  0.587
2011 Fleishman SJ, Leaver-Fay A, Corn JE, Strauch EM, Khare SD, Koga N, Ashworth J, Murphy P, Richter F, Lemmon G, Meiler J, Baker D. RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite. Plos One. 6: e20161. PMID 21731610 DOI: 10.1371/Journal.Pone.0020161  0.789
2011 Richter F, Leaver-Fay A, Khare SD, Bjelic S, Baker D. De novo enzyme design using Rosetta3. Plos One. 6: e19230. PMID 21603656 DOI: 10.1371/Journal.Pone.0019230  0.765
2011 Fleishman SJ, Khare SD, Koga N, Baker D. Restricted sidechain plasticity in the structures of native proteins and complexes. Protein Science : a Publication of the Protein Society. 20: 753-7. PMID 21432939 DOI: 10.1002/Pro.604  0.438
2010 Weerapana E, Wang C, Simon GM, Richter F, Khare S, Dillon MB, Bachovchin DA, Mowen K, Baker D, Cravatt BF. Quantitative reactivity profiling predicts functional cysteines in proteomes. Nature. 468: 790-5. PMID 21085121 DOI: 10.1038/Nature09472  0.687
2007 Khare SD, Dokholyan NV. Molecular mechanisms of polypeptide aggregation in human diseases. Current Protein & Peptide Science. 8: 573-9. PMID 18220844 DOI: 10.2174/138920307783018703  0.457
2007 Das R, Qian B, Raman S, Vernon R, Thompson J, Bradley P, Khare S, Tyka MD, Bhat D, Chivian D, Kim DE, Sheffler WH, Malmström L, Wollacott AM, Wang C, et al. Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins. 69: 118-28. PMID 17894356 DOI: 10.1002/Prot.21636  0.741
2007 Barton S, Jacak R, Khare SD, Ding F, Dokholyan NV. The length dependence of the polyQ-mediated protein aggregation. The Journal of Biological Chemistry. 282: 25487-92. PMID 17591778 DOI: 10.1074/Jbc.M701600200  0.543
2006 Khare SD, Caplow M, Dokholyan NV. FALS mutations in Cu, Zn superoxide dismutase destabilize the dimer and increase dimer dissociation propensity: a large-scale thermodynamic analysis. Amyloid : the International Journal of Experimental and Clinical Investigation : the Official Journal of the International Society of Amyloidosis. 13: 226-35. PMID 17107883 DOI: 10.1080/13506120600960486  0.403
2006 Khare SD, Dokholyan NV. Common dynamical signatures of familial amyotrophic lateral sclerosis-associated structurally diverse Cu, Zn superoxide dismutase mutants. Proceedings of the National Academy of Sciences of the United States of America. 103: 3147-52. PMID 16488975 DOI: 10.1073/pnas.0511266103  0.433
2005 Khare SD, Ding F, Gwanmesia KN, Dokholyan NV. Molecular origin of polyglutamine aggregation in neurodegenerative diseases. Plos Computational Biology. 1: 230-5. PMID 16158094 DOI: 10.1371/Journal.Pcbi.0010030  0.523
2005 Khare SD, Wilcox KC, Gong P, Dokholyan NV. Sequence and structural determinants of Cu, Zn superoxide dismutase aggregation. Proteins. 61: 617-32. PMID 16152647 DOI: 10.1002/Prot.20629  0.73
2004 Dixon RD, Chen Y, Ding F, Khare SD, Prutzman KC, Schaller MD, Campbell SL, Dokholyan NV. New insights into FAK signaling and localization based on detection of a FAT domain folding intermediate. Structure (London, England : 1993). 12: 2161-71. PMID 15576030 DOI: 10.1016/J.Str.2004.09.011  0.583
2004 Khare SD, Caplow M, Dokholyan NV. The rate and equilibrium constants for a multistep reaction sequence for the aggregation of superoxide dismutase in amyotrophic lateral sclerosis. Proceedings of the National Academy of Sciences of the United States of America. 101: 15094-9. PMID 15475574 DOI: 10.1073/pnas.0406650101  0.388
2004 Urbanc B, Cruz L, Ding F, Sammond D, Khare S, Buldyrev SV, Stanley HE, Dokholyan NV. Molecular dynamics simulation of amyloid beta dimer formation. Biophysical Journal. 87: 2310-21. PMID 15454432 DOI: 10.1529/Biophysj.104.040980  0.625
2004 Khatun J, Khare SD, Dokholyan NV. Can contact potentials reliably predict stability of proteins? Journal of Molecular Biology. 336: 1223-38. PMID 15037081 DOI: 10.1016/j.jmb.2004.01.002  0.496
2003 Khare SD, Ding F, Dokholyan NV. Folding of Cu, Zn superoxide dismutase and familial amyotrophic lateral sclerosis. Journal of Molecular Biology. 334: 515-25. PMID 14623191 DOI: 10.1016/J.Jmb.2003.09.069  0.523
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