Sagar Khare, Ph.D. - Publications

2006 University of North Carolina, Chapel Hill, Chapel Hill, NC 

58 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
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/  1
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  1
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  1
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  0.72
2018 Rubenstein AB, Blacklock K, Nguyen H, Case DA, Khare SD. Systematic comparison of Amber and Rosetta energy functions for protein structure evaluation. Journal of Chemical Theory and Computation. PMID 30240210 DOI: 10.1021/acs.jctc.8b00303  0.72
2017 Blacklock K, Yang L, Mulligan VK, Khare SD. A Computational Method for the Design of Nested Proteins by Loop-Directed Domain Insertion. Proteins. PMID 29250820 DOI: 10.1002/prot.25445  0.48
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  1
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  1
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  1
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  0.72
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  1
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  1
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  0.72
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  1
2016 Tinberg CE, Khare SD. Improving Binding Affinity and Selectivity of Computationally Designed Ligand-Binding Proteins Using Experiments. Methods in Molecular Biology (Clifton, N.J.). 1414: 155-71. PMID 27094290 DOI: 10.1007/978-1-4939-3569-7_9  1
2015 Khare SD, Whitehead TA. Introduction to the Rosetta Special Collection. Plos One. 10: e0144326. PMID 26714017 DOI: 10.1371/journal.pone.0144326  1
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  1
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  1
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  1
2014 Dash SK, Sharma M, Khare S, Kumar A. Carbon-Mercaptooctadecane/Carboxylated Multi-walled Carbon Nanotubes Composite Based Genosensor for Detection of Bacterial Meningitis. Indian Journal of Microbiology. 54: 170-7. PMID 25320418 DOI: 10.1007/s12088-013-0435-7  0.36
2014 Kumar S, Khare S, Saidullah B, Gandhoke I, Ram H, Singh S, Chauhan LS, Rai A. Appearance of L90I and N205S Mutations in Effector Domain of NS1 Gene of pdm (09) H1N1 Virus from India during 2009-2013. Advances in Virology. 2014: 861709. PMID 25309598 DOI: 10.1155/2014/861709  0.36
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  1
2014 Bhatt N, Khan N, Dash SK, Khare S, Kumar A. nspA gene as a specific genetic marker for detection of Neisseria meningitidis causing bacterial meningitis. Indian Journal of Biochemistry & Biophysics. 51: 211-4. PMID 25204083  0.36
2014 Singh S, Kaushal A, Khare S, Kumar P, Kumar A. Gold-mercaptopropionic acid-polyethylenimine composite based DNA sensor for early detection of rheumatic heart disease. The Analyst. 139: 3600-6. PMID 24875529 DOI: 10.1039/c4an00324a  0.36
2014 Singh S, Kaushal A, Khare S, Kumar A. mga genosensor for early detection of human rheumatic heart disease. Applied Biochemistry and Biotechnology. 173: 228-38. PMID 24639090 DOI: 10.1007/s12010-014-0836-z  0.36
2014 Singh S, Kumar A, Khare S, Mulchandani A, Rajesh. Single-walled carbon nanotubes based chemiresistive genosensor for label-free detection of human rheumatic heart disease Applied Physics Letters. 105. DOI: 10.1063/1.4902447  0.36
2014 Dash SK, Sharma M, Kumar A, Khare S. Carbon composite-based DNA sensor for detection of bacterial meningitis caused by Neisseria meningitidis Journal of Solid State Electrochemistry. 18: 2647-2659. DOI: 10.1007/s10008-014-2525-9  0.36
2013 Dash SK, Sharma M, Khare S, Kumar A. Quick diagnosis of human brain meningitis using omp85 gene amplicon as a genetic marker. Indian Journal of Microbiology. 53: 238-40. PMID 24426115 DOI: 10.1007/s12088-013-0371-6  0.36
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  1
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  1
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  1
2013 Dash SK, Sharma M, Khare S, Kumar A. rmpM genosensor for detection of human brain bacterial meningitis in cerebrospinal fluid. Applied Biochemistry and Biotechnology. 171: 198-208. PMID 23824531 DOI: 10.1007/s12010-013-0339-3  0.36
2013 Saurabh K, Gupta R, Khare S, Sharma S. Atypical subacute sclerosing panencephalitis with short onset latency. Indian Pediatrics. 50: 244-5. PMID 23474932 DOI: 10.1007/s13312-013-0044-x  0.36
2013 Dash SK, Sharma M, Khare S, Kumar A. Omp85 genosensor for detection of human brain bacterial meningitis. Biotechnology Letters. 35: 929-35. PMID 23471585 DOI: 10.1007/s10529-013-1161-2  0.36
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  1
2013 Gandhoke I, Hussain SA, Pasha ST, Chauhan LS, Khare S. Glycoprotein B genotyping in congenital/perinatal Cytomegalovirus infection in symptomatic infants. Indian Pediatrics. 50: 663-7. PMID 23255693 DOI: 10.1007/s13312-013-0199-5  0.36
2013 Hasan T, Khare S, Jain S, Gupta P, Sharma S. Retinal vasculature - An imaging based morphological study Journal of the Anatomical Society of India. 62: 146-156. DOI: 10.1016/j.jasi.2013.12.010  0.36
2012 Kaushal A, Kumar D, Khare S, Kumar A. speB gene as a specific genetic marker for early detection of rheumatic heart disease in human. Cellular and Molecular Biology (Noisy-Le-Grand, France). 58: 50-4. PMID 23273191 DOI: 10.1170/T920  0.36
2012 Dash SK, Sharma M, Khare S, Kumar A. rmpM gene as a genetic marker for human bacterial meningitis. Cellular and Molecular Biology (Noisy-Le-Grand, France). 58: 26-30. PMID 23273188 DOI: 10.1170/T917  0.36
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2005 Khare SD, Dmg F, Gwsnmesis KH, Dokhoiyan NV. Molecular origin of polygiutamine Plos Computational Biology. 1: 0230-0235.  1
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  1
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  1
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  1
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  1
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  1
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