Feng Ding

TitleAssistant Professor
InstitutionClemson University
DepartmentDepartment of Physics & Astronomy
Address118 Kinard Laboratory
Clemson, South Carolina 29634
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    1. Benhamou Goldfajn N, Tang H, Ding F. Substoichiometric Inhibition of Insulin against IAPP Aggregation Is Attenuated by the Incompletely Processed N-Terminus of proIAPP. ACS Chem Neurosci. 2022 Jun 15. PMID: 35704461.
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    2. Ren J, Andrikopoulos N, Velonia K, Tang H, Cai R, Ding F, Ke PC, Chen C. Chemical and Biophysical Signatures of the Protein Corona in Nanomedicine. J Am Chem Soc. 2022 Jun 01; 144(21):9184-9205. PMID: 35536591.
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    3. Tang H, Sun Y, Ding F. Hydrophobic/Hydrophilic Ratio of Amphiphilic Helix Mimetics Determines the Effects on Islet Amyloid Polypeptide Aggregation. J Chem Inf Model. 2022 04 11; 62(7):1760-1770. PMID: 35311274.
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    4. Tang H, Li Y, Kakinen A, Andrikopoulos N, Sun Y, Kwak E, Davis TP, Ding F, Ke PC. Graphene quantum dots obstruct the membrane axis of Alzheimer's amyloid beta. Phys Chem Chem Phys. 2021 Dec 22; 24(1):86-97. PMID: 34878460.
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    5. Liu Y, Zhang Y, Sun Y, Ding F. A buried glutamate in the cross-ß core renders ß-endorphin fibrils reversible. Nanoscale. 2021 Dec 02; 13(46):19593-19603. PMID: 34812835.
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    6. Nandakumar A, Wei W, Siddiqui G, Tang H, Li Y, Kakinen A, Wan X, Koppel K, Lin S, Davis TP, Leong DT, Creek DJ, Ding F, Song Y, Ke PC. Dynamic Protein Corona of Gold Nanoparticles with an Evolving Morphology. ACS Appl Mater Interfaces. 2021 Dec 08; 13(48):58238-58251. PMID: 34797630.
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    7. Saikia N, Yanez-Orozco IS, Qiu R, Hao P, Milikisiyants S, Ou E, Hamilton GL, Weninger KR, Smirnova TI, Sanabria H, Ding F. Integrative structural dynamics probing of the conformational heterogeneity in synaptosomal-associated protein 25. Cell Rep Phys Sci. 2021 Nov 17; 2(11). PMID: 34888535.
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    8. Kolimi N, Pabbathi A, Saikia N, Ding F, Sanabria H, Alper J. Out-of-Equilibrium Biophysical Chemistry: The Case for Multidimensional, Integrated Single-Molecule Approaches. J Phys Chem B. 2021 09 23; 125(37):10404-10418. PMID: 34506140.
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    9. Lee M, Ni N, Tang H, Li Y, Wei W, Kakinen A, Wan X, Davis TP, Song Y, Leong DT, Ding F, Ke PC. A Framework of Paracellular Transport via Nanoparticles-Induced Endothelial Leakiness. Adv Sci (Weinh). 2021 11; 8(21):e2102519. PMID: 34495564.
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    10. Simon-Baram H, Kleiner D, Shmulevich F, Zarivach R, Zalk R, Tang H, Ding F, Bershtein S. SAMase of Bacteriophage T3 Inactivates Escherichia coli's Methionine S-Adenosyltransferase by Forming Heteropolymers. mBio. 2021 08 31; 12(4):e0124221. PMID: 34340545.
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    11. Andrikopoulos N, Song Z, Wan X, Douek AM, Javed I, Fu C, Xing Y, Xin F, Li Y, Kakinen A, Koppel K, Qiao R, Whittaker AK, Kaslin J, Davis TP, Song Y, Ding F, Ke PC. Inhibition of Amyloid Aggregation and Toxicity with Janus Iron Oxide Nanoparticles. Chem Mater. 2021 Aug 24; 33(16):6484-6500. PMID: 34887621.
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    12. Li Y, Tang H, Zhu H, Kakinen A, Wang D, Andrikopoulos N, Sun Y, Nandakumar A, Kwak E, Davis TP, Leong DT, Ding F, Ke PC. Ultrasmall Molybdenum Disulfide Quantum Dots Cage Alzheimer's Amyloid Beta to Restore Membrane Fluidity. ACS Appl Mater Interfaces. 2021 Jun 30; 13(25):29936-29948. PMID: 34143617.
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    13. He H, Liu Y, Sun Y, Ding F. Misfolding and Self-Assembly Dynamics of Microtubule-Binding Repeats of the Alzheimer-Related Protein Tau. J Chem Inf Model. 2021 06 28; 61(6):2916-2925. PMID: 34032430.
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    14. Ma J, Saikia N, Godar S, Hamilton GL, Ding F, Alper J, Sanabria H. Ensemble Switching Unveils a Kinetic Rheostat Mechanism of the Eukaryotic Thiamine Pyrophosphate Riboswitch. RNA. 2021 Apr 16. PMID: 33863818.
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    15. Sun Y, Kakinen A, Wan X, Moriarty N, Hunt CPJ, Li Y, Andrikopoulos N, Nandakumar A, Davis TP, Parish CL, Song Y, Ke PC, Ding F. Spontaneous Formation of ß-sheet Nano-barrels during the Early Aggregation of Alzheimer's Amyloid Beta. Nano Today. 2021 Jun; 38. PMID: 33936250.
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    16. Sun Y, Huang J, Duan X, Ding F. Direct Observation of ß-Barrel Intermediates in the Self-Assembly of Toxic SOD128-38 and Absence in Nontoxic Glycine Mutants. J Chem Inf Model. 2021 02 22; 61(2):966-975. PMID: 33445870.
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    17. Basak S, Sakia N, Dougherty L, Guo Z, Wu F, Mindlin F, Lary JW, Cole JL, Ding F, Bowen ME. Probing Interdomain Linkers and Protein Supertertiary Structure In Vitro and in Live Cells with Fluorescent Protein Resonance Energy Transfer. J Mol Biol. 2021 03 05; 433(5):166793. PMID: 33388290.
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    18. Xing Y, Nandakumar A, Kakinen A, Sun Y, Davis TP, Ke PC, Ding F. Amyloid Aggregation under the Lens of Liquid-Liquid Phase Separation. J Phys Chem Lett. 2021 Jan 14; 12(1):368-378. PMID: 33356290.
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    19. Li Y, Tang H, Andrikopoulos N, Javed I, Cecchetto L, Nandakumar A, Kakinen A, Davis TP, Ding F, Ke PC. The membrane axis of Alzheimer's nanomedicine. Adv Nanobiomed Res. 2021 Jan; 1(1). PMID: 33748816.
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    20. Sun Y, Ding F. aB-Crystallin Chaperone Inhibits Aß Aggregation by Capping the ß-Sheet-Rich Oligomers and Fibrils. J Phys Chem B. 2020 11 12; 124(45):10138-10146. PMID: 33119314.
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    21. Chen P, Ding F, Cai R, Javed I, Yang W, Zhang Z, Li Y, Davis TP, Ke PC, Chen C. Amyloidosis Inhibition, a New Frontier of the Protein Corona. Nano Today. 2020 Dec; 35. PMID: 32728376.
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    22. Javed I, Zhang Z, Adamcik J, Andrikopoulos N, Li Y, Otzen DE, Lin S, Mezzenga R, Davis TP, Ding F, Ke PC. Accelerated Amyloid Beta Pathogenesis by Bacterial Amyloid FapC. Adv Sci (Weinh). 2020 Sep; 7(18):2001299. PMID: 32999841.
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    23. Koppel K, Tang H, Javed I, Parsa M, Mortimer M, Davis TP, Lin S, Chaffee AL, Ding F, Ke PC. Elevated amyloidoses of human IAPP and amyloid beta by lipopolysaccharide and their mitigation by carbon quantum dots. Nanoscale. 2020 Jun 18; 12(23):12317-12328. PMID: 32490863.
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    24. Miao Z, Adamiak RW, Antczak M, Boniecki MJ, Bujnicki J, Chen SJ, Cheng CY, Cheng Y, Chou FC, Das R, Dokholyan NV, Ding F, Geniesse C, Jiang Y, Joshi A, Krokhotin A, Magnus M, Mailhot O, Major F, Mann TH, Piatkowski P, Pluta R, Popenda M, Sarzynska J, Sun L, Szachniuk M, Tian S, Wang J, Wang J, Watkins AM, Wiedemann J, Xiao Y, Xu X, Yesselman JD, Zhang D, Zhang Y, Zhang Z, Zhao C, Zhao P, Zhou Y, Zok T, Zyla A, Ren A, Batey RT, Golden BL, Huang L, Lilley DM, Liu Y, Patel DJ, Westhof E. RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers. RNA. 2020 08; 26(8):982-995. PMID: 32371455.
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    25. Xing Y, Sun Y, Wang B, Ding F. Morphological Determinants of Carbon Nanomaterial-Induced Amyloid Peptide Self-Assembly. Front Chem. 2020; 8:160. PMID: 32211382.
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    26. Sun Y, Ding F. Thermo- and pH-responsive fibrillization of squid suckerin A1H1 peptide. Nanoscale. 2020 Mar 21; 12(11):6307-6317. PMID: 32108838.
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    27. Huma ZE, Javed I, Zhang Z, Bilal H, Sun Y, Hussain SZ, Davis TP, Otzen DE, Landersdorfer CB, Ding F, Hussain I, Ke PC. Nanosilver Mitigates Biofilm Formation via FapC Amyloidosis Inhibition. Small. 2020 05; 16(21):e1906674. PMID: 31984626.
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    28. Nandakumar A, Xing Y, Aranha RR, Faridi A, Kakinen A, Javed I, Koppel K, Pilkington EH, Purcell AW, Davis TP, Faridi P, Ding F, Ke PC. Human Plasma Protein Corona of Aß Amyloid and Its Impact on Islet Amyloid Polypeptide Cross-Seeding. Biomacromolecules. 2020 02 10; 21(2):988-998. PMID: 31909987.
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    29. Faridi A, Sun Y, Mortimer M, Aranha RR, Nandakumar A, Li Y, Javed I, Kakinen A, Fan Q, Purcell AW, Davis TP, Ding F, Faridi P, Ke PC. Graphene quantum dots rescue protein dysregulation of pancreatic ß-cells exposed to human islet amyloid polypeptide. Nano Res. 2019 Nov; 12(11):2827-2834. PMID: 31695851.
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    30. Kakinen A, Xing Y, Hegoda Arachchi N, Javed I, Feng L, Faridi A, Douek AM, Sun Y, Kaslin J, Davis TP, Higgins MJ, Ding F, Ke PC. Single-Molecular Heteroamyloidosis of Human Islet Amyloid Polypeptide. Nano Lett. 2019 09 11; 19(9):6535-6546. PMID: 31455083.
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    31. Javed I, Peng G, Xing Y, Yu T, Zhao M, Kakinen A, Faridi A, Parish CL, Ding F, Davis TP, Ke PC, Lin S. Inhibition of amyloid beta toxicity in zebrafish with a chaperone-gold nanoparticle dual strategy. Nat Commun. 2019 08 22; 10(1):3780. PMID: 31439844.
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    32. Sun Y, Kakinen A, Zhang C, Yang Y, Faridi A, Davis TP, Cao W, Ke PC, Ding F. Amphiphilic surface chemistry of fullerenols is necessary for inhibiting the amyloid aggregation of alpha-synuclein NACore. Nanoscale. 2019 Jun 12. PMID: 31188372.
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    33. Ke PC, Pilkington EH, Sun Y, Javed I, Kakinen A, Peng G, Ding F, Davis TP. Mitigation of Amyloidosis with Nanomaterials. Adv Mater. 2020 May; 32(18):e1901690. PMID: 31183916.
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    34. Sun Y, Kakinen A, Xing Y, Faridi P, Nandakumar A, Purcell AW, Davis TP, Ke PC, Ding F. Amyloid Self-Assembly of hIAPP8-20 via the Accumulation of Helical Oligomers, a-Helix to ß-Sheet Transition, and Formation of ß-Barrel Intermediates. Small. 2019 05; 15(18):e1805166. PMID: 30908844.
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    35. Sun Y, Kakinen A, Xing Y, Pilkington EH, Davis TP, Ke PC, Ding F. Nucleation of ß-rich oligomers and ß-barrels in the early aggregation of human islet amyloid polypeptide. Biochim Biophys Acta Mol Basis Dis. 2019 02 01; 1865(2):434-444. PMID: 30502402.
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    36. Kakinen A, Sun Y, Javed I, Faridi A, Pilkington EH, Faridi P, Purcell AW, Zhou R, Ding F, Lin S, Chun Ke P, Davis TP. Physical and Toxicological Profiles of Human IAPP Amyloids and Plaques. Sci Bull (Beijing). 2019 Jan 15; 64(1):26-35. PMID: 30662791.
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    37. Wang M, Sun Y, Cao X, Peng G, Javed I, Kakinen A, Davis TP, Lin S, Liu J, Ding F, Ke PC. Graphene quantum dots against human IAPP aggregation and toxicity in vivo. Nanoscale. 2018 Nov 01; 10(42):19995-20006. PMID: 30350837.
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    38. Faridi A, Sun Y, Okazaki Y, Peng G, Gao J, Kakinen A, Faridi P, Zhao M, Javed I, Purcell AW, Davis TP, Lin S, Oda R, Ding F, Ke PC. Mitigating Human IAPP Amyloidogenesis In Vivo with Chiral Silica Nanoribbons. Small. 2018 11; 14(47):e1802825. PMID: 30369028.
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    39. Yanez Orozco IS, Mindlin FA, Ma J, Wang B, Levesque B, Spencer M, Rezaei Adariani S, Hamilton G, Ding F, Bowen ME, Sanabria H. Identifying weak interdomain interactions that stabilize the supertertiary structure of the N-terminal tandem PDZ domains of PSD-95. Nat Commun. 2018 09 13; 9(1):3724. PMID: 30214057.
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    40. Wang B, Sun Y, Davis TP, Ke PC, Wu Y, Ding F. Understanding Effects of PAMAM Dendrimer Size and Surface Chemistry on Serum Protein Binding with Discrete Molecular Dynamics Simulations. ACS Sustain Chem Eng. 2018 Sep 04; 6(9):11704-11715. PMID: 30881771.
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    41. Sun Y, Ge X, Xing Y, Wang B, Ding F. ß-barrel Oligomers as Common Intermediates of Peptides Self-Assembling into Cross-ß Aggregates. Sci Rep. 2018 07 09; 8(1):10353. PMID: 29985420.
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    42. Sun Y, Ding F, Ming D. Nonnative Energetic Frustrations in Protein Folding at Residual Level: A Simulation Study of Homologous Immunoglobulin-like ß-Sandwich Proteins. Int J Mol Sci. 2018 May 18; 19(5). PMID: 29783701.
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    43. Ge X, Sun Y, Ding F. Structures and dynamics of ß-barrel oligomer intermediates of amyloid-beta16-22 aggregation. Biochim Biophys Acta Biomembr. 2018 09; 1860(9):1687-1697. PMID: 29550287.
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    44. Xing Y, Pilkington EH, Wang M, Nowell CJ, Kakinen A, Sun Y, Wang B, Davis TP, Ding F, Ke PC. Lysophosphatidylcholine modulates the aggregation of human islet amyloid polypeptide. Phys Chem Chem Phys. 2017 Nov 22; 19(45):30627-30635. PMID: 29115353.
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    45. Sun Y, Wang B, Ge X, Ding F. Distinct oligomerization and fibrillization dynamics of amyloid core sequences of amyloid-beta and islet amyloid polypeptide. Phys Chem Chem Phys. 2017 Oct 25; 19(41):28414-28423. PMID: 29038815.
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    46. Ge X, Kakinen A, Gurzov EN, Yang W, Pang L, Pilkington EH, Govindan-Nedumpully P, Chen P, Separovic F, Davis TP, Ke PC, Ding F. Zinc-coordination and C-peptide complexation: a potential mechanism for the endogenous inhibition of IAPP aggregation. Chem Commun (Camb). 2017 Aug 22; 53(68):9394-9397. PMID: 28745731.
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    47. Wang B, Pilkington EH, Sun Y, Davis TP, Ke PC, Ding F. Modulating protein amyloid aggregation with nanomaterials. Environ Sci Nano. 2017 Sep 01; 4(9):1772-1783. PMID: 29230295.
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    48. Wang B, Blin T, Käkinen A, Ge X, Pilkington EH, Quinn JF, Whittaker MR, Davis TP, Ke PC, Ding F. Brushed polyethylene glycol and phosphorylcholine for grafting nanoparticles against protein binding. Polym Chem. 2016 Dec 07; 7(45):6875-6879. PMID: 28348639.
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    49. Nedumpully-Govindan P, Kakinen A, Pilkington EH, Davis TP, Chun Ke P, Ding F. Stabilizing Off-pathway Oligomers by Polyphenol Nanoassemblies for IAPP Aggregation Inhibition. Sci Rep. 2016 Jan 14; 6:19463. PMID: 26763863.
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    50. Nedumpully-Govindan P, Yang Y, Andorfer R, Cao W, Ding F. Promotion or Inhibition of Islet Amyloid Polypeptide Aggregation by Zinc Coordination Depends on Its Relative Concentration. Biochemistry. 2015 Dec 22; 54(50):7335-44. PMID: 26603575.
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    51. Nedumpully-Govindan P, Gurzov EN, Chen P, Pilkington EH, Stanley WJ, Litwak SA, Davis TP, Ke PC, Ding F. Graphene oxide inhibits hIAPP amyloid fibrillation and toxicity in insulin-producing NIT-1 cells. Phys Chem Chem Phys. 2016 Jan 07; 18(1):94-100. PMID: 26625841.
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    52. Nedumpully-Govindan P, Jemec DB, Ding F. CSAR Benchmark of Flexible MedusaDock in Affinity Prediction and Nativelike Binding Pose Selection. J Chem Inf Model. 2016 06 27; 56(6):1042-52. PMID: 26252196.
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    53. Ge X, Ke PC, Davis TP, Ding F. A Thermodynamics Model for the Emergence of a Stripe-like Binary SAM on a Nanoparticle Surface. Small. 2015 Oct 07; 11(37):4894-9. PMID: 26191774.
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    54. DeFever RS, Geitner NK, Bhattacharya P, Ding F, Ke PC, Sarupria S. PAMAM dendrimers and graphene: materials for removing aromatic contaminants from water. Environ Sci Technol. 2015 Apr 07; 49(7):4490-7. PMID: 25786141.
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    55. Nedumpully-Govindan P, Ding F. Inhibition of IAPP aggregation by insulin depends on the insulin oligomeric state regulated by zinc ion concentration. Sci Rep. 2015 Feb 04; 5:8240. PMID: 25649462.
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    56. Radic S, Davis TP, Ke PC, Ding F. Contrasting effects of nanoparticle-protein attraction on amyloid aggregation. RSC Adv. 2015 Jan 01; 5(127):105498. PMID: 26989481.
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    57. Wang B, Seabrook SA, Nedumpully-Govindan P, Chen P, Yin H, Waddington L, Epa VC, Winkler DA, Kirby JK, Ding F, Ke PC. Thermostability and reversibility of silver nanoparticle-protein binding. Phys Chem Chem Phys. 2015 Jan 21; 17(3):1728-39. PMID: 25461673.
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    58. Geitner NK, Wang B, Andorfer RE, Ladner DA, Ke PC, Ding F. Structure-function relationship of PAMAM dendrimers as robust oil dispersants. Environ Sci Technol. 2014 Nov 04; 48(21):12868-75. PMID: 25279688.
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    59. Radic S, Nedumpully-Govindan P, Chen R, Salonen E, Brown JM, Ke PC, Ding F. Effect of fullerenol surface chemistry on nanoparticle binding-induced protein misfolding. Nanoscale. 2014 Jul 21; 6(14):8340-9. PMID: 24934397.
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    60. Nedumpully-Govindan P, Li L, Alexov EG, Blenner MA, Ding F. Structural and energetic determinants of tyrosylprotein sulfotransferase sulfation specificity. Bioinformatics. 2014 Aug 15; 30(16):2302-9. PMID: 24794930.
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    61. Ding F, Radic S, Chen R, Chen P, Geitner NK, Brown JM, Ke PC. Direct observation of a single nanoparticle-ubiquitin corona formation. Nanoscale. 2013 Oct 07; 5(19):9162-9. PMID: 23921560.
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    62. Radic S, Geitner NK, Podila R, Käkinen A, Chen P, Ke PC, Ding F. Competitive binding of natural amphiphiles with graphene derivatives. Sci Rep. 2013; 3:2273. PMID: 23881402.
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    63. Ding F, Dokholyan NV. Incorporating backbone flexibility in MedusaDock improves ligand-binding pose prediction in the CSAR2011 docking benchmark. J Chem Inf Model. 2013 Aug 26; 53(8):1871-9. PMID: 23237273.
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