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Khare lab authors underlined.

Preprints and manuscripts under review/revision:

Lubin, J.H.,  Zardecki, C., Dolan, E.M., Lu, C., Shen, Z., Dutta, S., Westbrook, J.D., Hudson, B.P., Goodsell, D.S., Williams, J.K., Voigt, M.,  Sarma, V.Xie, L., Venkatachalam, T., Arnold, S.,  Helena, L., Alvarado, A., Catalfano, K., Khan, A., McCarthy, E., Staggers, S., Tinsley, B., Trudeau, A., Singh, J., Whitmore, L., Zheng, H., Benedek, M., Currier, J., Dresel, M., Duvvuru, A., Dyszel, B., Fingar, E., Hennen, E.M., Kirsch, M., Khan, A.A., Labrie-Cleary, C., Laporte, S., Lenkeit, E., Martin, K., Orellana, M., Ortiz-Alvarez de la Campa, M., Paredes, I., Wheeler, B., Rupert, A., Sam, A., See, K., Zapata, S.S., Craig, P.A., Hall, B.L., Jiang, J., Koeppe, J.R., Mills, S.A., Pikaart, M.J., Roberts, R., Bromberg, Y., Hoyer, J.S., Duffy, S., Tischfield, J., Ruiz, F.X., Arnold, E., Baum, J., Sandberg, J., Brannigan, G., Khare, S.D., Burley, S.K. Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first six months of the COVID-19 pandemic.



54. Schuster, B.S., Regy, R.M., Dolan, E.M., Ranganath, A.K., Jovic, N., Khare, S.D., Shi, Z., Mittal, J. Biomolecular Condensates: Sequence Determinants of Phase Separation, Microstructural Organization, Enzymatic Activity, and Material Properties. J. Phys. Chem. B 2021. [Journal]

53. Jiang, V., Khare, S.D., Banta, S. Computational Structure Prediction Provides a Plausible Mechanism for Electron Transfer by the Outer Membrane Protein Cyc2 from Acidithiobacillus ferrooxidans.


52. Burley, S.K., Bromberg, Y., Craig, P., Duffy, S., Dutta, S., Hall, B.L., Hudson, B.P., Jiang, J., Khare, S.D., Koeppe, J.R., Lubin, J.H., Mills, S.A., Pikaart, M.J., Roberts, R., Sarma, V., Singh, J., Tischfield, J.A., Xie, L., Zardecki, C. (2020). Virtual Boot Camp: COVID-19 evolution and structural biology. Biochem Mol Biol Educ, 48, 511–513. [Journal]

51. Hansen, W. A.; Khare, S. D. Recent Progress in Designing Protein-Based Supramolecular Assemblies. Curr. Opin. Struct. Biol. 2020, 63, 106−114. [Journal]

50. Leman, J.K., Weitzner B.D., Lewis, S.M., Adolf-Bryfogle, J., Alam, N., Alford, R.F., Aprahamian M., Baker, D. Barlow, K.A., Barth, P., Basanta, B., Bender, B.J, Blacklock, K., Bonet, J., Boyken, S.E., Bradley, P., Bystroff C., Conway P., Cooper S., Correia, B.E., Coventry, B., Das R., De Jong, R.M., DiMaio, F., Dsilva, L., Dunbrack, R., Ford, A.S., Frenz, B., Fu, D.Y., Geniesse, C., Goldschmidt, L., Gowthaman, R., Gray, J.J., Gront D., Guffy, S., Horowitz, S., Huang, P., Huber, T., Jacobs T.M., Jeliazkov, J.R., Johnson, D.K., Kappel, K., Karanicolas, J., Khakzad H., Khar, K.R., Khare, S.D., Khatib, F., Khramushin A., King, I.C., Kleffner, R., Koepnick, B., Kortemme, T., Kuenze, G., Kuhlman, B., Kuroda, D., Labonte J.W., Lai, J.K., Lapidoth, G., Leaver-Fay, A., Lindert, S., Linsky, T., London, N., Lubin, J.H., Lyskov, S., Maguire, J., Malmström, L., Marcos, E., Marcu, O., Marze, N.A., Meiler, J., Moretti, R., Mulligan, V.K., Nerli, S., Norn, C., Ó’Conchúir, S., Ollikainen, N., Ovchinnikov, S., Pacella, M.S., Pan, X., Park, H., Pavlovicz R.E., Pethe, M., Pierce, B.G., Pilla. K.B., Raveh, B., Renfrew, D.P., Roy Burman, S.S., Rubenstein A., Sauer, M.F., Scheck, A., Schief, W., Schueler-Furman, O., Sedan, Y., Sevy, A.M., Sgourakis, N.G., Shi, L., Siegel, J.B., Silva, D., Smith, S., Song, Y., Stein, A., Szegedy, M., Teets, F.D., Thyme, S.B., Wang, R.Y., Watkins, A., Zimmerman, L., Bonneau, R. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nat Methods 17, 665–680 (2020). [Journal]

49. Yang, F.; Totsingan, F.; Dolan, E.; Khare, S.D.; Gross, R.A. Protease-catalyzed l-aspartate oligomerization: substrate selectivity and computational modeling. ACS Omega 2020, 5, 4403−4414. [Journal]

48. Agrawal, D.K.; Dolan, E.M.; Hernandez, N.E.; Blacklock, K.M.; Khare, S.D.; Sontag, E.D. Mathematical Models of Protease-Based Enzymatic Biosensors. ACS Synth. Biol. 2020, 9, 198–208. [Journal]


47. N. E. Hernández*, W. A. Hansen*, D. Zhu, M. E. Shea, M. Khalid, V. Manichev, M. Putnins, M. Chen, A. G. Dodge, L. Yang, M. Banal, T. Gustafsson, L. C. Feldman, S-H Lee, L. P. Wackett, W. Dai and S. D. Khare‡ “Stimulus-responsive self-assembly of protein-based fractals by computational design” (2019) Nature Chemistry in press (* = equal contribution)[preprint: bioRxiv]

46. N. Yasuike, K. M. Blacklock, Huixin Lu, A.S.I. Jaikaran, S. McDonald, M. Uppalapati, S. D. Khare G. A. Woolley “Photoswitchable affinity reagents: Computational design and efficient red-light switching” (2019) ChemPhotoChem in press [Journal]

45. M. A. Pethe*, A. B. Rubenstein*, S. D. Khare “Data-driven supervised learning of a viral protease specificity landscape from deep sequencing and molecular simulations”  (2019) Proc. Natl. Acad. Sci. USA [PubMed] [preprint: bioRxiv] (* = equal contribution)


44. A. B. Rubenstein, K. M. Blackock, H. Ngyuen, D. A. Case, S. D. Khare“Systematic comparison of Amber and Rosetta energy functions for protein structure evaluation” (2018) J. Chem. Theor. Comput. 4:6015-6025

[PubMed] [preprint: chemRxiv] (‡ = co-corresponding authors)

43. J. K. Williams, X. Yang, T. B. Atieh, M. P. Olson, S. D. Khare, J. Baum “Multi-Pronged Interactions Underlie Inhibition of α-Synuclein Aggregation by β-Synuclein” (2018) J. Mol. Biol. 430:2360-2371[PubMed]

42. K. M. Blacklock, L. Yang, V. K. Mulligan, S. D. Khare “A computational method for the design of nested proteins using loop-directed domain insertion” (2018) Proteins: Struct. Func. Bioinfo.86:354-369 [PubMed]

41. R. D. Barrows, K. M. Blacklock, P. R. Rablen, S. D. Khare , S. Knapp “Computational Assessment of Thioether Isosteres” (2018) J. Mol. Graph. Model. 80:282-292 [Pubmed]

40. K. M. Blacklock, B. J. Yachnin, G. A. Woolley, S. D. Khare“Computational design of a photocontrolled cytosine deaminase” (2018) J. Am. Chem. Soc. 140:14-17 [PubMed]


39. E. Moore, D. Zorine, W. A. Hansen, S. D. Khare, R. Fasan “Enzyme stabilization via computationally guided protein stapling” (2017)  Proc. Natl. Acad. Sci. USA 114: 12472-12477 [PubMed] ( = co-corresponding authors)

38. L. Yang, E. M. Dolan, S. K. Tan, T. Lin, E. D. Sontag and S. D. Khare “Computational design of a stimulus responsive multi-enzyme supramolecular assembly” (2017) ChemBioChem 18:2000-2006 [PubMed]

37. K. M. Davis, K. R. Schramma, W. A. Hansen, J-P. Bacik, S. D. Khare, M. R. Seyedsayamdost, N. Ando “Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition” (2017) Proc. Natl. Acad. Sci. USA 114:10420-10425 [PubMed]

36. G. M. Moriarty, M. P. Olson, T. Atieh, M. Janowska, S. D. Khare, J. Baum “Formation of fibrils by beta-synuclein at mildly acidic pH mediated by charged interaction clusters” (2017) J. Biol. Chem. 292:16368-16379 (‡ = co-corresponding authors)[PubMed]

35. A. E. Owens, I. de Paola, W. A. Hansen, Y-W Liu, S. D. Khare, and R. Fasan “Design and Evolution of a Macrocyclic Peptide Inhibitor of the Sonic Hedgehog/Patched Interaction” (2017) J. Am. Chem. Soc. 139:12559-12568 [PubMed]

34. A. B. Rubenstein, M. A. Pethe and S. D. Khare “MFPred: Rapid and accurate prediction of multispecificity at protein-peptide interfaces using self-consistent mean-field theory” (2017) PLoS Comput. Biol. 13:e1005614 [PubMed]

33. W. A. Hansen and S. D. Khare “Benchmarking a protein design method for introducing multinuclear metal ion-binding sites at oligomeric protein interfaces” (2017) Protein Sci. 26:1584-1594 [PubMed]

32. B. J. Yachnin and S. D. Khare “Designing a circularly permuted carboxypeptidase G2 enzyme for an autoinhibited enzyme drug” (2017) Protein Eng. Des. Sel. 30: 321-331 [PubMed]

31. M. A. Pethe, A. B. Rubenstein and S. D. Khare “Large-scale structure-based prediction and identification of novel protease substrates using computational protein design” (2017) J. Mol. Biol. 429:220-236 [PubMed]

30. C. E. Tinberg, and S. D. Khare “Computational design of ligand binding proteins” (2017) Methods Mol. Biol. 1529:363-373.[PubMed]


29. C. E. Tinberg, and S. D. Khare “Improving Binding Affinity and Selectivity of Computationally Designed Ligand-Binding Proteins Using Experiments.” (2016) Methods Mol. Biol. 1414:155-171.[PubMed]

28. W. A. Hansen, J. H. Mills, and S. D. Khare “Computational design of metalloproteins using unnatural amino acids”. (2016) Methods Mol. Biol. 1414:173-85.[PubMed]


27. 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 “CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge” (2015) J. Chem. Inf. Model. 56:1022-1031[PubMed]

26. Nanda V, Senn S, Pike DH, Rodriguez-Granillo A, Hansen WA, Khare SD, Noy D. “Structural principles for computational and de novo design of 4Fe-4S metalloproteins.” (2015) Biochim. Biophys. Acta. 15: 201-207 .[PubMed]

25. Bednar D, Beerens K, Sebestova E, Bendl J, Khare SD, Chaloupkova R, Prokop Z, Brezovsky J, Baker D, Damborsky J. “FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants” (2015) PLoS Comput. Biol. 11:e1004556  [PubMed]

24. S. D. Khare, Whitehead TA. “Introduction to the Rosetta Special Collection.” (2015) PLoS One 10: e0144326 (= co-corresponding authors)[PubMed]


23. P. J. Gresien amd S. D. Khare, “Computational redesign of metalloenzymes for introducing new activities” (2014) Methods Mol. Biol. 1216: 265-273 [PubMed]


22. S. D. Khare and S. J. Fleishman “Emerging themes in the computational design of novel enzymes and protein-protein interfaces” (2013) FEBS Lett., 587: 1147-1154 . (= co-corresponding authors) [PubMed]

21. J. H. Mills, S. D. Khare, J. M. Bolduc, F. Forouhar, V. K. Mulligan, S. Lew, J. Seetharaman, L. Tong, B. L. Stoddard, and D. Baker “Computational Design of an Unnatural Amino Acid Dependent Metalloprotein with Atomic Level Accuracy” (2013) J. Am. Chem. Soc. 135: 13393-13399 [PubMed]

20. C. E. Tinberg*, S. D. Khare*, J. Dou, L. Doyle, J. Nelson, A. Schena, W. Jankowski, C. G. Kalodimos, K. Johnsson, B. L. Stoddard, and D. Baker, “Computational Design of Ligand Binding Proteins with High Affinity and Selectivity.” (2013) Nature 501: 212-216 * = contributed equally [PubMed]

19. I. Cherny, P. J. Greisen, Y. Ashani, S. D. Khare, G. Oberdorfer, H. Leader, D. Baker, D. S. Tawfik, “Engineering V-type nerve agents detoxifying enzymes using computationally focused libraries.” (2013) ACS Chem. Biol. 8: 2394-2403 [PubMed]


18. S. D. Khare*, Y. Kipnis*, P. J. Greisen*, R. Takeuchi, Y. Ashani, M. Goldsmith, Y. Song, J. L. Gallaher, I. Silman, H. Leader, J. L. Sussman, B. L. Stoddard, D. S. Tawfik, and D. Baker, “Redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis” Nature Chem. Biol., 8: 294-300 (2012). *contributed equally

17. F. Richter, R. Blomberg, S. D. Khare, G. Kiss, A. P. Kuzin, A. J. Smith, J. L. Gallaher, Z. Pianowski, R. C. Helgeson, A. Grjasnow, R. Xiao, J. Seetharaman, M. Su, S. Vorobiev, S. Lew, F. Forouhar, G. J. Kornhaber, J. F. Hunt, G. T. Montelione, L. Tong, K. N. Houk, D. Hilvert, and D. Baker, “ Computational design of catalytic dyads and oxyanion holes for ester hydrolysis” J. Am. Chem. Soc. 134: 16197-207 (2012).

16. S. J. Fleishman, S. D. Khare, N. Koga, and D. Baker, “Restricted sidechain plasticity in the structures of native proteins and complexes” Protein Science, 20: 753-7 (2011).

15. F. Richter, A. Leaver-Fay, S. D. Khare, S. Bjelic, and D. Baker, “De novo enzyme design using Rosetta3” PLoS One, 6: e19230 (2011).

14. S. J. Fleishman, A. Leaver-Fay, J. E. Corn, E.-M. Strauch, S. D. Khare, N. Koga, J. Ashworth, P. Murphy, F. Richter, G. Lemmon, J. Meiler, and D. Baker, “RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite” PLoS One, 6: e20161 (2011).

13. E. Weerapana, C. Wang, G. M. Simon, F. Richter, S. Khare, M. B. D. Dillon, D. A. Bachovchin, K. Mowen, D. Baker, and B. F. Cravatt, “Quantitative reactivity profiling predicts functional cysteines in proteomes” Nature, 468: 790-5 (2010).

12. R. Das, B. Qian, S. Raman, R. Vernon, J. Thompson, P. Bradley, S. Khare, M. D. Tyka, D. Bhat, D. Chivian, D. E. Kim, W. H. Sheffler, L. Malmström, A. M. Wollacott, C. Wang, I. Andre, and D. Baker, “Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home.” Proteins 69: Suppl 8, 118-28 (2007).

11. S. Barton, R. Jacak, S. D. Khare, F. Ding, and N. V. Dokholyan, “The length dependence of the polyQ- mediated protein aggregation” J. Biol. Chem., 282: 25487-25492 (2007).

10. S. D. Khare, and N. V. Dokholyan, “Molecular mechanisms of polypeptide aggregation in human diseases” Curr. Protein Pept. Sci., 8: 573-579 (2007).

9. S. D. Khare, and N. V. Dokholyan, “Common dynamical signatures of FALS-associated structurally- diverse Cu, Zn superoxide dismutase mutants” Proc. Natl. Acad. Sci. USA, 103: 3147-3152 (2006).

8. S. D. Khare, M. Caplow, and N. V. Dokholyan, “FALS mutations in Cu, Zn superoxide dismutase destabilize the dimer and increase dimer dissociation propensity: a large-scale thermodynamic analysis” Amyloid, 13: 226-235 (2006).

7. S. D. Khare, K. C. Wilcox, P. Gong, and N. V. Dokholyan, “Sequence and structural determinants of Cu, Zn superoxide dismutase aggregation” Proteins: Struct. Funct. Bioinfo., 61: 617-632 (2005).

6. S. D. Khare, F. Ding, K. N. Gwanmesia, and N. V. Dokholyan, “Molecular origin of polyglutamine- mediated aggregation in neurodegenerative diseases” PLoS Comp. Biol., 1: e30 (2005).

5. S. D. Khare, M. Caplow, and N. V. Dokholyan, “The rate and equilibrium constants for a multi-step reaction sequence for the aggregation of superoxide dismutase in ALS” Proc. Natl. Acad. Sci. USA, 101: 15094-15099 (2004).

4. J. Khatun*, S. D. Khare*, and N. V. Dokholyan, “Can contact potentials reliably predict stability of proteins?” J. Mol. Biol., 336: 1223-1238 (2004). *contributed equally

3. R. D. S. Dixon, Y. Chen, F. Ding, S. D. Khare, K. C. Prutzman, M. D. Schaller, S. L. Campbell, and N. V. Dokholyan, “New insights into FAK signaling and localization based on detection of a FAT domain folding intermediate” Structure, 12: 2161-2171 (2004).

2. B. Urbanc, L. Cruz, F. Ding, D. Sammond, S. Khare, S. V. Buldyrev, H. E. Stanley, and N. V. Dokholyan, “Molecular dynamics simulation of Amyloid-beta dimer formation” Biophys. J., 87: 2310-2321 (2004).

1. S. D. Khare, F. Ding, and N. V. Dokholyan, “Folding of Cu, Zn superoxide dismutase and Familial Amyotrophic Lateral Sclerosis” J. Mol. Biol., 334: 515-525 (2003).

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