{"id":34,"date":"2021-04-14T03:48:53","date_gmt":"2021-04-14T03:48:53","guid":{"rendered":"http:\/\/dlab.clemson.edu\/?page_id=34"},"modified":"2026-04-07T03:07:50","modified_gmt":"2026-04-07T03:07:50","slug":"publications","status":"publish","type":"page","link":"https:\/\/dlab.clemson.edu\/?page_id=34","title":{"rendered":"Publications"},"content":{"rendered":"

External publication lists: Pubmed<\/a>, Google Scholar<\/a>, Web of Science<\/a><\/p>\n

\n\"\"<\/a> \"\"<\/a> \"\"<\/a> \"\"<\/a> \"\"<\/a> \"\"<\/a> \"\"<\/a> \"\"<\/a> \"\"<\/a> \"\"<\/a> \"\"<\/a> \"\"<\/a> \"\"<\/a><\/p>\n

207. Y. Sun, N. Andrikopoulos, F. Ding*, P.C. Ke*, “An endogenous beta-endorphin corona confers neuroprotection against Alzheimer’s amyloidogenesis”, Neural Regeneration Research (2026) doi: 10.4103\/NRR.NRR-D-25-01700<\/a><\/p>\n

206. S. Wu, L. Zhou, X. Kang, G. Huang, Y. Cha, J. Shen, C. Wang, K. H. Lackey, D. Kim, F. Ding*, P. Chen*, “Peptide Aptamer-Enabled Nanoplasmonic Digital Immunoassay for Ultra-sensitive Cytokine Sensing in Early Inflammation and Immune Modulation”, ACS Sensors, in press (2026) doi: 10.1021\/acssensors.5c04120<\/a><\/p>\n

205. F. Huang, Y. Zhang, X. Zhang, J. Xu, C. Wang, X. Huang, S. Liu*, F. Ding*, Y. Sun*, “Structural and energetic effects of disulfide mediation on the conformational dynamics of human calcitonin”, International Journal of Biological Macromolecules (Elsevier), 338(2): 149880 (2026) doi: 10.1016\/j.ijbiomac.2025.149880<\/a><\/p>\n

204. Z. Zhang, L. Hayes, T. Hou, F. Ding, “Parallel In-Register Contact Propensity Predicts the Amyloidogenicity of ADan and ABri in Familial Dementias”, International Journal of Biological Macromolecules (Elsevier), 338(1): 149627 (2026) doi: 10.1016\/j.ijbiomac.2025.149627<\/a><\/p>\n

203. K. Bhandari, Y. Sun, H. Tang, P. Ke, F. Ding, “A Global Thermodynamic-Kinetic Model Capturing the Hallmarks of Liquid-Liquid Phase Separation and Amyloid Aggregation”, Cell Reports Physical Science, 103031 (2025)doi: 10.1016\/j.xcrp.2025.103031<\/a> <\/p>\n

202. Z. Song, K. Bhandari, T. Hou, F. Ding, “APOE genotype difference in the biphasic modulation of amyloid-\u03b2 aggregation by direct binding and lowering the nucleation barrier”, Biomacromolecules, 26(12): 8494\u20138507 (2025) doi: 10.1021\/acs.biomac.5c01323<\/a><\/p>\n

201. D.Y. Zhang, J. Wang, G. Huang, M. Dokholyan, S. Willcox, J. Griffith, F. Ding, N.V. Dokholyan, “Apolipoprotein E (APOE) regulates the transport of monosialotetrahexosylganglioside (GM1)”, Journal of Biological Chemistry, 301(11): 110778 (2025) doi: 10.1016\/j.jbc.2025.110778<\/a><\/p>\n

200. Z. Lv, H. Xu, Y. Zhang, H. Tang, F. Ding, F. Huang, Y. Sun, “Conformational Ensemble Dynamics of Intrinsically Disordered Full-Length \u03b1- and \u03b2-Synuclein Monomers”, J Chem Inf Model., 65(17):9261-9273 (2025) doi: 10.1021\/acs.jcim.5c01602.<\/a><\/p>\n

199. H. Tang, Y. Sun, L. Wang, P.C. Ke, F. Ding, “Emergence of Compact Oligomers inside the Small-World Network of TDP-43 Condensates”, J Phys Chem Lett. 16(31):7797-7806 (2025) doi: 10.1021\/acs.jpclett.5c01627.<\/a><\/p>\n

198. X. Zhang, H. Xu, H. Tang, Z. Lv, Y. Zou, F. Huang, F. Ding*, and Y. Sun*, “The Glycine-Rich Region as a Flexible Molecular Glue Promoting hPrP106\u2013145 Aggregation into \u03b2-Sheet Structures”, JCIM, 65(13): 7054\u20137064 (2025) doi: 10.1021\/acs.jcim.5c00785<\/a><\/p>\n

197. Y. Wang, G. Huang, X. Liang, N. Andrikopoulos, H. Tang, F. Ding*, P. C. Ke*, Y. Li*, “Microglial Clearance of Alzheimer\u2019s Amyloid-Beta Obstructed by Nanoplastics”, Environmental Science: Nano, 12, 3247-3260 (2025) doi: 10.1039\/D5EN00291E<\/a><\/p>\n

196. Y. Sun, N. Andrikopoulos, G. Zhang, Y. Liu, X. Liang, D. Li, X. Suo, Y. Wang, Y. Li, C. Wang, Y. Li, P. C. Ke, F. Ding, “Formation of a \u03b2-Endorphin Corona Mitigates Alzheimer\u2019s Amyloidogenesis”, Small, 21(26):e2409392 (2025) doi: 10.1002\/smll.202409392<\/a><\/p>\n

195. H. Tang, N. Andrikopoulos, Y. Li, S. Ke, Y. Sun*, F. Ding*, P.C. Ke*, “Emerging biophysical origins and pathogenic implications of amyloid oligomers”, Nature Communications, 16: 2937 (2025) doi: 10.1038\/s41467-025-58335-y<\/a><\/p>\n

194. A. Gatch, F. Ding, “Cross-interaction with amyloid-\u03b2 drives pathogenic structural transformation within the amyloidogenic core region of TDP-43”, ACS Chemical Neuroscience, 16(8): 1565\u20131581, (2025) doi: 10.1021\/acschemneuro.5c00084<\/a><\/p>\n

193. S. Parris, J. Lovell, F. Ding, Z. Zhang, J. Olvey, J. Olvey II, J. Schmutz, J. Grimwood, A. Sreedasyam,S. Kumar, Z. Li, P. Joshi, J. Jenkins, C. Plott, A. Stewart, J. Webber, W. Stiller, D. Jones, C. Saski, “Polyploidy-Mediated Variations in Glutamate Receptor Proteins Linked to Fusarium Wilt Resistance in Upland Cotton”, The Plant Journal, 122(1): e70125 (2025) doi: 10.1111\/tpj.70125<\/a><\/p>\n

192. Z. Zhang, G. Huang, S. Gupta, E. Sargent, H. Tang, F. Ding, “Determinants for Sub-stoichiometric Inhibition of IAPP and A-Beta Amyloid Aggregations by Bri2 BRICHOS”, ACS Chemical Neuroscience, 16(6): 1150\u20131160 (2025) doi:10.1021\/acschemneuro.4c00839 <\/a><\/p>\n

191. X. Liang, G. Huang, Y. Wang, N. Andrikopoulos, H. Tang, F. Ding*, Y. Li*, P.C. Ke*, “Polystyrene Nanoplastics Hitch-Hike the Gut-Brain Axis to Exacerbate Parkinson’s Pathology”, ACS Nano, 19(5): 5475\u20135492 (2025) doi: 10.1021\/acsnano.4c13914<\/a><\/p>\n

190. H. Xu, X. Zhang, Z. Lv, F. Huang, Y. Zou, C. Wang, F. Ding*, and Y. Sun*, “Computational exploration of the self-aggregation mechanisms of phenol-soluble modulins \u03b21 and \u03b22 in Staphylococcus aureus biofilms”, Colloids Surf B Biointerfaces, 248: 114498 (2025) doi: 10.1016\/j.colsurfb.2025.114498<\/a><\/p>\n

189. R. K. Goutam, G. Huang, E. Medina, F. Ding, W. J. Edenfield, and H. Sanabria, “Impact of Frequent ARID1A Mutations on Protein Stability: Insights into Cancer Pathogenesis”, Scientific Reports, 15: 3072 (2025) doi: 10.1038\/s41598-025-87103-7<\/a><\/p>\n

188. F. Huang, X, Fan, H. Xu, Z. Lv, Y. Zou, J. Lian, F. Ding*, Y. Sun*, “Computational insights into the aggregation mechanism of human calcitonin”, International Journal of Biological Macromolecules (Elsevier), 294: 139520 (2025) doi: 10.1016\/j.ijbiomac.2025.139520<\/a><\/p>\n

187. Bu F, Adam Y, Adamiak RW, Antczak M, de Aquino BRH, Badepally NG, Batey RT, Baulin EF, Boinski P, Boniecki MJ, Bujnicki JM, Carpenter KA, Chacon J, Chen SJ, Chiu W, Cordero P, Das NK, Das R, Dawson WK, DiMaio F, Ding F, Dock-Bregeon AC, Dokholyan NV, Dror RO, Dunin-Horkawicz S, Eismann S, Ennifar E, Esmaeeli R, Farsani MA, Ferr\u00e9-D’Amar\u00e9 AR, Geniesse C, Ghanim GE, Guzman HV, Hood IV, Huang L, Jain DS, Jaryani F, Jin L, Joshi A, Karelina M, Kieft JS, Kladwang W, Kmiecik S, Koirala D, Kollmann M, Kretsch RC, Kurci\u0144ski M, Li J, Li S, Magnus M, Masquida B, Moafinejad SN, Mondal A, Mukherjee S, Nguyen THD, Nikolaev G, Nithin C, Nye G, Pandaranadar Jeyeram IPN, Perez A, Pham P, Piccirilli JA, Pilla SP, Pluta R, Poblete S, Ponce-Salvatierra A, Popenda M, Popenda L, Pucci F, Rangan R, Ray A, Ren A, Sarzynska J, Sha CM, Stefaniak F, Su Z, Suddala KC, Szachniuk M, Townshend R, Trachman RJ 3rd, Wang J, Wang W, Watkins A, Wirecki TK, Xiao Y, Xiong P, Xiong Y, Yang J, Yesselman JD, Zhang J, Zhang Y, Zhang Z, Zhou Y, Zok T, Zhang D, Zhang S, \u017by\u0142a A, Westhof E, Miao Z., “RNA-Puzzles Round V: blind predictions of 23 RNA structures”, Nature Methods, 22 (2), 399-411 (2025) doi: 10.1038\/s41592-024-02543-9<\/a><\/p>\n

186. F. Huang, J. Yan, H. Xu, Y. Wang, X. Zhang, Y. Zou, J. Lian, F. Ding, Y. Sun, “Exploring the Impact of Physiological C-Terminal Truncation on \u03b1-Synuclein Conformations to Unveil Mechanisms Regulating Pathological Aggregation”, JCIM, 64(22): 8616\u20138627 (2024) doi: 10.1021\/acs.jcim.4c01839<\/a><\/p>\n

185. G. Huang, Z. Song, Y. Xu, Y. Sun, F. Ding, “Deciphering the Morphological Difference of Amyloid-\u03b2 Fibrils in Familial and Sporadic Alzheimer’s Diseases”, JCIM, 64(20): 8024\u20138033 (2024) doi: 10.1021\/acs.jcim.4c01471<\/a><\/p>\n

184. H. Tang, Y. Sun, L. Wang, P.C. Ke, F. Ding, “Uncovering intermolecular interactions driving the liquid-liquid phase separation of TDP-43 low complexity domain via atomistic dimerization simulations”, JCIM, 64(19):7590-7601 (2024) doi:10.1021\/acs.jcim.4c00943<\/a><\/p>\n

183. F. Huang, J. Yan, X. Zhang, H. Xu, J. Lian, X. Yang, C. Wang*, F. Ding*, Y. Sun*, “Computational Insights into the Aggregation Mechanism and Amyloidogenic Core of Aortic Amyloid Medin Polypeptide”, Colloids and Surfaces B: Biointerfaces, 244: 114192(2024) doi:10.1016\/j.colsurfb.2024.114192<\/a><\/p>\n

182. Z. Song, H. Tang, A. Gatch, Y. Sun and Feng Ding, “Islet Amyloid Polypeptide Fibril Catalyzes Amyloid-\u03b2 Aggregation by Promoting Fibril Nucleation Rather than Direct Axial Growth”, International Journal of Biological Macromolecules (Elsevier), 279(1): 135137 (2024) doi: 10.1016\/j.ijbiomac.2024.135137<\/a><\/p>\n

181. A. Gatch and F. Ding, “TDP-43 Promotes Amyloid-beta Toxicity by Delaying Fibril Maturation via Direct Molecular Interaction”, ACS Chemical Neuroscience, 15(15): 2936\u20132953 (2024) doi: 10.1021\/acschemneuro.4c00334<\/a><\/p>\n

180. X. Fan, X. Zhang, J. Yan, H. Xu, W. Zhao, F. Ding*, F. Huang*, Y. Sun*, “Computational Investigation of Co-Aggregation and Cross-Seeding between A\u03b2 and hIAPP Underpinning the Crosstalk in Alzheimer\u2019s Disease and Type-2 Diabetes”, J. Chem. Inf. Model., 64(13): 5303\u20135316 (2024) doi:10.1021\/acs.jcim.4c00859<\/a><\/p>\n

179. F. Huang, J. Huang, J. Yan, Y. Liu, J. Lian, Q. Sun, F. Ding, Y. Sun,”Molecular Insights into the Effects of F16L and F19L Substitutions on the Conformation and Aggregation Dynamics of Human Calcitonin”, J. Chem. Inf. Model., 64, 11, 4500\u20134510 (2024) doi:10.1021\/acs.jcim.4c00553 <\/a><\/p>\n

178. A. Nandakumar, H. Tang, N. Andrikopoulos, J. F. Quinn, F. Ding,* P. C. Ke* and Y. Li*, “Controlling nanoparticle-induced endothelial leakiness with the protein corona”, Nanoscale, 6(19):9348-9360 (2024) doi:10.1039\/D4NR01311E<\/a><\/p>\n

177. Y. Wang, X. Liang, N. Andrikopoulos, H. Tang, F. He, X. Yin, Y. Li, F. Ding, G. Peng, M. Mortimer, P.C. Ke, “Remediation of Metal Oxide Nanotoxicity with a Functional Amyloid”, Advanced Science, 11(23):2310314 (2024) doi:10.1002\/advs.202310314<\/a><\/p>\n

176. A. Chaari, N. Saikia, P. Paul, M. Yousef, F. Ding, M. Ladjimi, “Experimental and computational investigation of the effect of Hsc70 structural variants on inhibiting amylin aggregation”, Biophysical Chemistry, 309:107235 (2024) doi:10.1016\/j.bpc.2024.107235<\/a><\/p>\n

175. F. Huang, X. Fan, Y. Wang, Y. Zou, J. Lian, C. Wang, F. Ding*, Y. Sun*, “Computational insights into the cross-talk between medin and A\u03b2: implications for age-related vascular risk factors in Alzheimer’s disease”, Brief. Bioinform.,25(2):bbad526 (2024) doi:10.1093\/bib\/bbad526<\/a><\/p>\n

174. Y. Li, N. Ni, M. Lee, W. Wei, N. Andrikopoulos, A. Kakinen, T. P. Davis, Y. Song*, F. Ding*, D. T. Leong* and P. Ke*, “Endothelial leakiness elicited by amyloid protein aggregation”, Nature Communications,15, Article number: 613 (2024) doi:10.1038\/s41467-024-44814-1<\/a><\/p>\n

173. J. Yan, Y. Wang, X. Fan, Y. Zou, F. Ding*, F. Huang*, Y. Sun*, “Deciphering the influence of Y12L and N17H substitutions on the conformation and oligomerization of human calcitonin”, Soft Matter, 20:693-703 (2024) doi:10.1039\/d3sm01332d<\/a><\/p>\n

172. F. Huang, Y. Liu, Y. Wang, J. Xu, J. Lian, Y. Zou, C. Wang*, F. Ding* and Y. Sun*, “Co-aggregation of \u03b1-synuclein with Amyloid-\u03b2 Stabilizes \u03b2-sheet-rich Oligomers and Enhances the Formation of \u03b2-barrels”, Physical Chemistry Chemical Physics, 25(46): 31604-31614 (2023) doi:10.1039\/D3CP04138G <\/a><\/p>\n

171. X. Liang, N. Andrikopoulos, H. Tang, Y. Wang, F. Ding* and P.C. Ke*, “Nanoplastic stimulates the amyloidogenesis of Parkinson\u2019s alpha-synuclein NACore”, Small, 20(14):e2308753 (2023) doi:10.1002\/smll.202308753<\/a><\/p>\n

170. F. Huang, X. Fan, Y. Wang, C. Wang, Y. Zou, J. Lian*, F. Ding*, Y. Sun*, “Unveiling Medin Folding and Dimerization Dynamics and Conformations via Atomistic Discrete Molecular Dynamics Simulations”, Journal of Chemical Information and Modeling, 63(20): 6376\u20136385 (2023) doi: 10.1021\/acs.jcim.3c01267 <\/a><\/p>\n

169. G. Huang, H. Tang, Y. Liu, C. Zhang, P. C. Ke, Y. Sun, F. Ding, “Direct Observation of Seeded Conformational Conversion of hIAPP In Silico Reveals the Mechanisms for Morphological Dependence and Asymmetry of Fibril Growth”, Journal of Chemical Information and Modeling, (63)18: 5863\u20135873 (2023) doi: 10.1021\/acs.jcim.3c00898<\/a><\/p>\n

168. S. Cao, Z. Song, J. Rong, N. Andrikopoulos, X. Liang, Y. Wang, G. Peng*, F. Ding*, P. C. Ke*, Spike Protein Fragments Promote Alzheimers Amyloidogenesis, ACS Applied Materials & Interfaces, 15(34): 40317\u201340329 (2023) doi: 10.1021\/acsami.3c09815<\/a><\/p>\n

167. Z. Zhang, G. Huang, Z. Song, A.J. Gatch, F. Ding , “Amyloid Aggregation and Liquid-Liquid Phase Separation from the Perspective of Phase Transitions”, J. Phys. Chem. B, 127(28): 6241\u20136250 (2023) doi: 10.1021\/acs.jpcb.3c01426<\/a><\/p>\n

166. Y. Wang, J. Xu, J. Yan, X. Fan, G. Wei, C. Wang, F. Ding*, Y. Sun*, “SEVI Inhibits A\u03b2 Amyloid Aggregation by Capping the \u03b2-Sheet Elongation Edges”, Journal of Chemical Information and Modeling, 63(11):3567-3578 (2023) doi: 10.1021\/acs.jcim.3c00414<\/a><\/p>\n

165. Huang F., Wang Y.,  Zhang Y., Wang C., Lian J., Ding F.*,  Sun Y.*, “Dissecting the Self-assembly Dynamics of Imperfect Repeats in \u03b1-Synuclein”, Journal of Chemical Information and Modeling, 63(11):3591-3600 (2023) doi: 10.1021\/acs.jcim.3c00533<\/a><\/p>\n

164. Song Z., Gatch A.J., Sun, Y. and Ding, F., “Differential binding and conformational dynamics of tau microtubule-binding repeats with a preformed amyloid-\u03b2 fibril seed”, ACS Chemical Neuroscience, 14(7):1321-1330 (2023) doi: 10.1021\/acschemneuro.3c00014<\/a><\/p>\n

163. Zheng C., Wei Y., Zhang P., Xu L., Zhang Z., Lin K., Hou J., Lv X., Ding Y., Chiu Y., Jain A., Islam N., Malovannaya A., Wu Y., Ding F., Xu H., Sun M., Chen X., and Chen Y., “CRISPR\/Cas9 screen uncovers functional translation of cryptic lncRNA-encoded open reading frames in human cancer”, Journal of Clinical Investigation, 133(5):e159940 (2023) doi: 10.1172\/JCI159940<\/a><\/p>\n

162. Andrikopoulos N., Li Y., Nandakumar A., Quinn J., Davis T., Ding F.*, Saikia N.*, Ke P.C.*, “Zinc-Epigallocatechin-3-gallate Network-Coated Nanocomposites against the Pathogenesis of Amyloid-Beta”, ACS Applied Materials & Interfaces, 15, 6, 7777\u20137792 (2023) doi:10.1021\/acsami.2c20334<\/a><\/p>\n

161. S. Basak, N. Saikia, D. Kwun, U. B. Choi, F. Ding, M. E. Bowen, “Different Forms of Disorder in NMDA-Sensitive Glutamate Receptor Cytoplasmic Domains Are Associated with Differences in Condensate Formation”, Biomolecules, 13(1):4 doi:10.3390\/biom13010004<\/a>(2023)<\/p>\n

160. Y. Liu, Y. Wang, Y. Zhang, Y. Zou, G. Wei, F. Ding* and Y. Sun*, “Structural perturbation of monomers determines the amyloid aggregation propensity of calcitonin variants”, Journal of Chemical Information and Modeling, 63, 1, 308\u2013320 doi:10.1021\/acs.jcim.2c01202:<\/a>(2023)<\/p>\n

159. Y. Zhang, Y. Wang, Y. Liu, G. Wei, F. Ding, Y. Sun, “Molecular Insights into the Misfolding and Dimerization Dynamics of the Full-length \u03b1-synuclein from Atomistic Discrete Molecular Dynamics Simulations”, ACS Chemical Neuroscience, 13, 21, 3126\u20133137 doi:10.1021\/acschemneuro.2c00531<\/a>(2022)<\/p>\n

158. J. He, L. Zhou, G. Huang, J. Shen, W. Chen, C. Wang, A. Kim, Z. Zhang, W. Cheng, S. Dai, F. Ding,* and P. Chen*, “Enhanced Label-Free Nanoplasmonic Cytokine Detection in SARS-CoV-2 Induced Inflammation Using Rationally Designed Peptide Aptamer”, ACS Applied Materials & Interfaces, 14, 43, 48464\u201348475 doi:10.1021\/acsami.2c14748<\/a> (2022)<\/p>\n

157. Y. Xing, N. Andrikopoulos, Z. Zhang, Y. Sun, P.C. Ke, F. Ding, “Modulating nanodroplet formation en route to fibrillization of amyloid peptides with designed flanking sequences”, Biomacromolecules, 23(10):4179-4191, doi:10.1021\/acs.biomac.2c00642<\/a> (2022)<\/p>\n

156. G.L. Hamilton, N. Saikia, S. Basak, F.S. Welcome, F. Wu, J. Kubiak, C. Zhang, Y. Hao, C.A.M. Seidel, F. Ding*, H. Sanabria* and M.E. Bowen*, “Fuzzy Supertertiary Interactions within PSD-95 Enable Ligand Binding”, eLife, 11: e77242, doi:10.7554\/eLife.77242<\/a> (2022) The accompanied Insight<\/a> article.<\/p>\n

155. Gumna J, Antczak M, Adamiak RW, Bujnicki JM, Chen SJ, Ding F, Ghosh P, Li J, Mukherjee S, Nithin C, Pachulska-Wieczorek K, Ponce-Salvatierra A, Popenda M, Sarzynska J, Wirecki T, Zhang D, Zhang S, Zok T, Westhof E, Miao Z, Szachniuk M, Rybarczyk A., “Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models”, International Journal of Molecular Sciences, doi: 10.3390\/ijms23179630<\/a> (2022)<\/p>\n

154. W. Wei, Y. Li, M. Lee, N. Andrikopoulos, S. Lin, C. Chen, D. Leong, F. Ding, Y. Song, and P. Ke, “Anionic Nanoplastic Exposure Induces Endothelial Leakiness”, Nature Communications, 13: 4757, doi:10.1038\/s41467-022-32532-5<\/a> (2022) *Featured in Editors\u2019 Highlights: \u201cTranslational and Clinical Research\u201d<\/a> of Nat Comm.<\/p>\n

153. Y. Wang, Y. Liu, Y. Zhang, G. Wei, F. Ding, Y. Sun, “Molecular Insights into the Oligomerization Dynamics and Conformations of Amyloidogenic and Non-Amyloidogenic Amylin from Discrete Molecular Dynamics Simulations”, Physical Chemistry Chemical Physics, 24, 21773-21785, doi:10.1039\/D2CP02851D<\/a> (2022)<\/p>\n

152. Y. Liu, Y. Wang, C. Tong, G. Wei, F. Ding*, Y. Sun*, “Molecular Insights into the Self-assembly of Block Copolymer Suckerin Polypeptides into Nanoconfined \u03b2-sheets”, Small, 18(34): 2202642, doi: 10.1002\/smll.202202642<\/a> (2022)<\/p>\n

151. N. Benhamou Goldfajn, H. Tang, F. Ding, “Sub-Stoichiometric Inhibition of Insulin against IAPP Aggregation is Attenuated by the Incompletely Processed N-Terminus of proIAPP”, ACS Chemical Neuroscience, 13(13): 2006\u20132016 (2022) doi:10.1021\/acschemneuro.2c00231 <\/a><\/p>\n

150. J. Ren, K. Velonia, N. Andrikopoulos, H. Tang, F. Ding, P. C. Ke, C. Chen, “Chemical and Biophysical Signatures of the Protein Corona in Nanomedicine”, Journal of The American Chemical Society, 144(21): 9184\u20139205 (2022) doi:10.1021\/jacs.2c02277<\/a><\/p>\n

149. H. Tang, Y. Sun, F. Ding, “The Hydrophobic\/Hydrophilic Ratio of Amphiphilic Helix Mimetics Determines the Effects on Islet Amyloid Polypeptide Aggregation”, Journal of Chemical Information and Modeling, 62(7): 1760\u20131770 (2022) doi:10.1021\/acs.jcim.1c01566<\/a><\/p>\n

148. H. Tang, Y. Li, A. Kakinen, N. Andrikopoulos, Y. Sun, E. Kwak, T. P. Davis, F. Ding* and P. C. Ke*, “Graphene Quantum Dots Obstruct the Membrane Axis of Alzheimer\u2019s Amyloid Beta”, Physical Chemistry Chemical Physics, 24, 86-97 (2022) doi: 10.1039\/D1CP04246G<\/a><\/p>\n

147. A. Nandakumar, W. Wei , G. Siddiqui, H. Tang, Y. Li , A. Kakinen, X. Wan, K. Koppel, S. Lin, T. Davis, D. Leong, D. Creek, F. Ding, Y. Song, P. C. Ke, “Dynamic Protein Corona of Gold Nanoparticles with An Evolving Morphology”, ACS Appl. Mater. Interfaces, 13, 48, 58238\u201358251 (2021) doi: 10.1021\/acsami.1c19824<\/a><\/p>\n

146. Y. Liu, Y. Zhang, Y. Sun and F. Ding, “A Buried Glutamate in the Cross-\u03b2 Core Renders \u03b2-endorphin Fibrils Reversible”, Nanoscale, 13, 19593-19603 (2021) doi:10.1039\/D1NR05679D<\/a><\/p>\n

145. N. Saikia, I. S. Yanez-Orozco, R. Qiu, P. Hao, S. Milikisiyants, E. Ou, G. L. Hamilton, K. R. Weninger, T. Smirnova, H. Sanabria, and F. Ding, “Integrative structural dynamics probing of the conformational heterogeneity in synaptosomal-associated protein 25”, Cell Reports Physical Science 2:100616 (2021) doi:10.1016\/j.xcrp.2021.100616<\/a><\/p>\n

144. N. Kolimi, A. Pabbathi, N. Saikia, F. Ding, H. Sanabria, J. Alper, “Out-of-Equilibrium Biophysical Chemistry: The Case for Multidimensional, Integrated Single-Molecule Approaches”, J. Phys. Chem. B, 125, 37, 10404\u201310418 (2021) doi:10.1021\/acs.jpcb.1c02424<\/a><\/p>\n

143. M. Lee,\u2020 N. Ni,\u2020 H. Tang,\u2020 Y. Li,\u2020 W. Wei, A. Kakinen, X. Wan, T. P. Davis, Y. Song,* D. T. Leong,* F. Ding* and P. C. Ke*, “A Framework of Paracellular Transport via Nanoparticles-Induced Endothelial Leakiness”, Advanced Science, 2102519 (2021) doi:10.1002\/advs.202102519<\/a><\/p>\n

142. N. Andrikopoulos, Z. Song, X. Wan, A. Douek, I. Javed, C. Fu, X. Changkui, Y. Xing, F. Xin, Y. Li, A. Kakinen, K. Koppel, R. Qiao, A. Whittaker, J. Kaslin, T. Davis*, Y. Song*, F. Ding*, P.C. Ke*, “Inhibition of Amyloid Aggregation and Toxicity with Janus Iron Oxide Nanoparticles”, Chem. Mater., 33, 16, 6484\u20136500 (2021) doi: 10.1021\/acs.chemmater.1c01947<\/a><\/p>\n

141. H. Simon-Baram, D. Kleiner, F. Shmulevich, R. Zarivach, R. Zalk, H. Tang, F. Ding, S. Bershtein, “SAMase of bacteriophage T3 inactivates E. coli\u2019s methionine S-adenosyltransferase by forming hetero-polymers”, mBio, Vol. 12, No. 4 (2021) doi: 10.1128\/mBio.01242-21<\/a><\/p>\n

140. Y. Li, H. Tang, H. Zhu, A. Kakinen, D. Wang, N. Andrikopoulos, Y. Sun, A. Nandakumar, E. Kwak, T. Davis, D. Leong, F. Ding, P. C. Ke, “Ultrasmall Molybdenum Disulfide Quantum Dots Cage Alzheimer\u2019s Amyloid Beta to Restore Membrane Fluidity”, ACS Appl. Mater. Interfaces, 13(25): 29936\u201329948 (2021) doi: 10.1021\/acsami.1c06478<\/a><\/p>\n

139. H. He, Y. Liu, Y. Sun, F. Ding, “The Misfolding and Self-assembly Dynamics of Microtubule-binding Repeats of the Alzheimer-related Protein Tau”, J. Chem. Info. Model, 61(6): 2916\u20132925 (2021) doi: 10.1021\/acs.jcim.1c00217<\/a><\/p>\n

138. J. Ma, N. Saikia, S. Godar, G.L. Hamilton, F. Ding*, J. Alper*, H. Sanabria*, “Ensemble Switching Unveils a Kinetic Rheostat Mechanism of the Eukaryotic Thiamine Pyrophosphate Riboswitch”, RNA, 27(7): 771\u2013790 (2021) doi: 10.1261\/rna.075937.120<\/a><\/p>\n

137. Y. Sun, A. Kakinen, X. Wan, N. Moriarty, C.P.J. Hunt, Y. Li, N. Andrikopoulos, A. Nandakumar, T.P. Davis, C.L. Parish, Y. Song, P. C. Ke and F. Ding, \u201cSpontaneous Formation of \u03b2-sheet Nano-barrels during the Early Aggregation of Alzheimer\u2019s Amyloid Beta\u201d, Nano Today, 38, 101125 (2021) doi: 10.1016\/j.nantod.2021.101125<\/a><\/p>\n

136. Y. Sun, J. Huang, X. Duan and F. Ding, \u201cDirect Observation of \u03b2-barrel Intermediates in the Self-assembly of Toxic SOD128-38 and Absence in Non-toxic Glycine Mutants\u201d, J. Chem. Info. Model, 61, 2, 966\u2013975 (2021) doi: 10.1021\/acs.jcim.0c01319<\/a><\/p>\n

135. S. Basak, N. Saikia, L. Dougherty, Z. Guo, F. Wu, F. A. Mindlin, J. W. Lary, J. L. Cole, F. Ding & M. E. Bowen, \u201cProbing interdomain linkers and protein supertertiary structure in vitro and in live cells with fluorescent protein resonance energy transfer\u201d, J. Mol. Biol., 433(5): 166793
\n(2021) doi: doi.org\/10.1016\/j.jmb.2020.166793<\/a><\/p>\n

134. Y. Xing, A. Nandakumar, A. Kakinen, Y. Sun, T.P. Davis, P. C. Ke, and F. Ding, \u201cAmyloid Aggregation under the Lens of Liquid-Liquid Phase Separation\u201d, J. Phys. Chem. Lett., 12, XXX, 368\u2013378 (2021)doi: doi.org\/10.1021\/acs.jpclett.0c02567<\/a><\/p>\n

133. Y. Li, H. Tang, N. Andrikopoulos, I. Javed, L. Cecchetto, A. Nandakumar, A. Kakinen, T.P. Davis, F. Ding, and P. Ke, \u201cThe Membrane Axis of Alzheimer\u2019s Nanomedicine\u201d, Advanced NanoBiomed Research, 1, 2000040 (2021) doi: doi.org\/10.1002\/anbr.202000040 <\/a><\/p>\n

132. Chen P, Ding F, Cai R, Javed I, Yang W, Zhang Z, Li Y, Davis TP, Ke PC, Chen C., \u201cAmyloidosis Inhibition, a New Frontier of the Protein Corona\u201d, Nano Today, 35:100937 (2020) doi: 10.1016\/j.nantod.2020.100937<\/a><\/p>\n

131. Y. Sun, F. Ding, \u201c\u03b1B-Crystallin Chaperone Inhibits A\u03b2 Aggregation by Capping the \u03b2-Sheet-Rich Oligomers and Fibrils\u201d, J. Phys. Chem. B, 124:10138-10146 (2020) doi: 10.1021\/acs.jpcb.0c07256.<\/a><\/p>\n

130. I Javed,Z Zhang, J Adamcik, N Andrikopoulos, Y Li, DE Otzen, S Lin, R Mezzenga, TP Davis, F Ding* and P Ke*, \u201cAccelerated Amyloid Beta Pathogenesis by Bacterial Amyloid FapC\u201d, Advanced Science, 7, 2001299 (2020) doi: doi.org\/10.1002\/advs.202001299 <\/a>
\n\u2013 Featured as the Cover<\/a>.<\/p>\n

129. K. Koppel, H. Tang, I. Javed, M. Parsa, M. Mortimer, T.P. Davis, S. Lin, A.L. Chaffee, F. Ding* and P.C. Ke*, \u201cElevated Amyloidoses of Human IAPP and Amyloid Beta by Lipopolysaccharide and Their Mitigation by Carbon Quantum Dots\u201d, Nanoscale, 12, 12317-12328 (2020) doi: 10.1039\/D0NR02710C <\/a><\/p>\n

128. Community\/Group Publication \u2014 Miao Z, Adamiak RW, Antczak M, Boniecki MJ, Bujnicki JM, 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., \u201cRNA-Puzzles Round IV: 3D Structure Predictions of Four Ribozymes and Two Aptamers\u201d, RNA, 26(8): 982\u2013995 (2020) doi: 10.1261\/rna.075341.120<\/a><\/p>\n

127. Y. Xing, Y. Sun, B. Wang, & F. Ding, \u201cMorphological Determinants of Carbon Nanomaterial-Induced Amyloid Peptide Self-Assembly\u201d, Frontiers in Chemistry, 8: 160 (2020) DOI: 10.3389\/fchem.2020.00160 <\/a>PMCID:PMC7076083<\/a><\/p>\n

126. Y. Sun, F. Ding, \u201cThermo- and pH-Responsive Fibrillization of Squid Suckerin A1H1 Peptide\u201d, Nanoscale, 12<\/strong>, 6307 \u2013 6317 (2020) DOI: 10.1039\/C9NR09271D<\/a><\/p>\n

125. A Nandakumar, Y Xing, R Aranha, A Faridi, A Kakinen, I Javed, K Koppel, E Pilkington, A Purcell, T Davis, P Faridi, F Ding, PC Ke, \u201cHuman Plasma Protein Corona of A\u03b2 Amyloid and Its Impact on IAPP Cross-Seeding\u201d, Biomacromolecules, 21, 988-998 (2020) DOI: 10.1021\/acs.biomac.9b01650<\/a><\/p>\n

124. Z Huma,I Javed, Z Zhang, H Bilal, Y Sun, SZ Hussain, TP Davis, DE Otzen, CB Landersdorfer, F Ding, I Hussain and PC Ke, \u201cNano Silver Mitigates Biofilm Formation via FapC Amyloidosis Inhibition\u201d, Small, 1906674-1906683 (2019) DOI: 10.1002\/smll.201906674<\/a><\/p>\n

123. A Faridi, Y Sun, M Mortimer, RR Aranha, A Nandakumar, Y Li, I Javed, A Kakinen, Q Fan, AW Purcell, TP Davis,* F Ding,*  P Faridi,* and P Ke*, \u201cGraphene quantum dots rescue protein dysregulation of pancreatic \u03b2-cells exposed to human islet amyloid polypeptide\u201d, Nano Research, 12(11), 2827\u20132834 (2019) DOI: 10.1007\/s12274-019-2520-7 <\/a><\/p>\n

122. A Kakinen, Y Xing, NDH Arachchi, I Javed, L Feng, A Faridi, AM Douek, Y Sun, J Kaslin, TP Davis*, MJ Higgins*, F Ding*, and P Ke*, \u201cSingle-molecular hetero-amyloidosis of human islet amyloid polypeptide\u201d, Nano Lett, 19(9), 6535-6546 (2019) DOI: 10.1021\/acs.nanolett.9b02771 <\/a><\/p>\n

121. I Javed, G Peng, Y Xing, T Yu, M Zhao, A Kakinen, A Faridi, CL Parish, F Ding*, TP Davis*, P Ke* and S Lin*, \u201cInhibition of Amyloid Beta Toxicity in Zebrafish with A Chaperone-Gold Nanoparticle Dual Strategy\u201d, Nature Communications, 10, 3780 (2019) DOI: 10.1038\/s41467-019-11762-0 <\/a><\/p>\n

120. Y. Sun, A. Kakinen, C. Zhang, Y. Yang, A. Faridi, T. P. Davis, W. Cao, P. C. Ke and F. Ding, \u201cAmphiphilic Surface Chemistry of Fullerenols Is Necessary for Inhibiting the Amyloid Aggregation of Alpha-Synuclein NACore\u201d, Nanoscale, 11, 11933 \u2013 11945 (2019) DOI: 10.1039\/C9NR02407G <\/a><\/p>\n

119. P.C. Ke, E.H. Pilkington, Y. Sun, I. Javed, A. Kakinen, G. Peng, F. Ding, T.P. Davis, \u201cMitigation of Amyloidosis with Nanomaterials\u201d, Advanced Materials, 32(18):e1901690, (2020) DOI: 10.1002\/adma.201901690<\/a>
\n-Featured as the Cover<\/a> story.<\/p>\n

118. Y. Sun, A. Kakinen, Y. Xing, P. Faridi, A. Nandakumar, A.W. Purcell, T.P. Davis, P.C. Ke, and F. Ding, \u201cAmyloid self-assembly of hIAPP8-20 via the accumulation of helical oligomers, alpha-helix to beta-sheet transition, and formation of \u03b2-barrel intermediates\u201d, Small, 5(18):e1805166, (2019) DOI: 10.1002\/smll.201805166 <\/a>
\n\u2013 Featured as the Cover<\/a>.<\/p>\n

117. Y. Sun, A. Kakinen, Y. Xing, E.H. Pilkington, T.P. Davis, P. Ke, & F. Ding, \u201cNucleation of \u03b2-rich Oligomers and \u03b2-barrels in the Early Aggregation of Human Islet Amyloid Polypeptide\u201d, BBA-Molecular Basis of Disease, 1865 (2), 434-444, DOI: 10.1016\/j.bbadis.2018.11.021 <\/a> (2019)<\/p>\n

116. A. Kakinen, Y. Sun, I. Javed, A. Faridi, E.H. Pilkington, P. Faridi, A.W. Purcell, R. Zhou, F. Ding, S. Lin, P. Ke, and T. P. Davis, \u201cPhysical and Toxicological Profiles of Human IAPP Amyloids and Plaques\u201d, Science Bulletin, 64(1): 26-35 DOI: 10.1016\/j.scib.2018.11.012<\/a> (2019)<\/p>\n

115. M. Wang, Y. Sun, X. Cao, G. Peng, I. Javed, A. Kakinen, T.P. Davis, S. Lin, J. Liu, F. Ding, and P. Ke, \u201cGraphene Quantum Dots against Human IAPP Aggregation and Toxicity in Vivo\u201d, Nanoscale 10, 19995, DOI: 10.1039\/C8NR07180B <\/a> (2018)<\/p>\n

114. A. Faridi,Y. Sun, Y. Okazaki, G. Peng, J. Gao, A. Kakinen, P. Faridi, M. Zhao, I. Javed, A.W. Purcell, T.P. Davis, S. Lin, R. Oda, F. Ding, P. Ke, \u201cMitigating Human IAPP Amyloidogenesis in Vivo with Chiral Silica Nanoribbons\u201d, Small, 14, 1802825, DOI: 10.1002\/smll.201802825 <\/a>(2018)<\/p>\n

113. I.Y. Orozco , F. Mindlin , J. Ma , B. Levesque , B. Wang , M. Spencer , G. Hamilton , S.R. Adariani , F. Ding*, M. Bowen*, and H. Sanabria*, \u201cIdentifying Weak Interdomain Interactions that Stabilize the Supertertiary Structure of the N-Terminal Tandem PDZ Domains of PSD-95\u201d, Nature Communication 9: 3724, DOI: 10.1038\/s41467-018-06133-0<\/a>, (2018)<\/p>\n

112. B. Wang, Y. Sun, T. Davis, P.C. Ke, Y. Wu, and F. Ding, \u201cUnderstanding the Effects of PAMAM Dendrimer Size and Surface Chemistry on Serum Protein Binding with Discrete Molecular Dynamics Simulations\u201d, ACS Sustainable Chemistry & Engineering, 6 (9),11704\u201311715, DOI: 10.1021\/acssuschemeng.8b01959 <\/a>, (2018)<\/p>\n

111. Y. Sun, X. Ge , Y. Xing, Bo Wang, and F. Ding, \u201c\u03b2-barrel Oligomers as Common Intermediates of Peptides Self-Assembling into Cross-\u03b2 Aggregates\u201d, Scientific Reports 8: 10353, DOI: 10.1038\/s41598-018-28649-7<\/a> (2018)<\/p>\n

110. Pilkington E.P., Gustafsson O.J.R., Xing Y., Hernandez-Fernaud J., Zampronio C., Kakinen A., Faridi A., Ding F., Wilson P., Ke P.C. and Davis T.P., \u201cProfiling the Serum Protein Corona of Fibrillar Human Islet Amyloid Polypeptide\u201d, ACS Nano, 12, 6066\u22126078 (2018) DOI: 10.1021\/acsnano.8b02346<\/a>
\n-Featured as Journal Front Cover <\/a>.<\/p>\n

109. Sun Y., Ding F., Ming D., \u201cNonnative Energetic Frustrations in Protein Folding at Residual Level: A Simulation Study of Homologous Immunoglobulin-like \u03b2-Sandwich Protein\u201d, Int J Mol Sci., 19(5), pii: E1515 (2018) DOI: 10.3390\/ijms19051515 <\/a>.<\/p>\n

108. X. Ge., Y. Sun and F. Ding, \u201cStructures and Dynamics of \u03b2-barrel Oligomer Intermediates of Amyloid-beta16-22 Aggregation\u201d, BBA Biomembranes, 1860(9): 1687-1697 (2018) DOI: 10.1016\/j.bbamem.2018.03.011<\/a><\/p>\n

107. X. Ge., Y. Yang, Y. Sun, W. Cao and F. Ding, \u201cIslet Amyloid Polypeptide Promotes Amyloid-beta Aggregation by Binding-induced Helix-unfolding of the Amyloidogenic Core\u201d, ACS Chem. Neurosci., 9(5):967-975 (2018)DOI: 10.1021\/acschemneuro.7b00396<\/a><\/p>\n

106. A. Kakinen, J. Adamcik, B. Wang, X. Ge, R. Mezzenga, T.P. Davis, F. Ding, and P. Ke, \u201cNanoscale inhibition of polymorphic and ambidextrous IAPP amyloid aggregation with small molecules\u201d, Nano Research, 11(7): 3636\u20133647 (2018)[download]<\/a> DOI: 10.1007\/s12274-017-1930-7<\/a><\/p>\n

105. Williams, B., Zhao, B., Tandon, A., Ding, F., Weeks, K. M., Zhang, Q., and Dokholyan, N. V. \u201cStructure modeling of RNA using sparse NMR constraints\u201d, Nucleic Acids Research, 45(22):12638-12647 (2017) DOI: 10.1093\/nar\/gkx1058<\/a><\/p>\n

104. I. Javed, Y. Sun, J. Adamcik, B. Wang, A. Kakinen, E. Pilkington, F. Ding, R. Mezzenga, T. Davis, Thomas; P. Ke, \u201cCo-fibrillization of pathogenic and functional amyloid proteins with gold nanoparticles against amyloidogenesis\u201d, Biomacromolecules, 18, 4316\u20134322 (2017) DOI: 10.1021\/acs.biomac.7b01359<\/a><\/p>\n

103. Y. Xing, E. H. Pilkington, M. Wang, C. Nowell, A. Kakinen, Y. Sun, B. Wang, T. P. Davis, F. Ding and P. C. Ke, \u201cLysophosphatidylcholine modulates the aggregation of human islet amyloid polypeptide\u201d, Phys. Chem. Chem. Phys., 19, 30627-30635, 2017, DOI: 10.1039\/C7CP06670H<\/a><\/p>\n

102. E. Pilkington, M. Lai, X. Ge, W. Stanley, B. Wang, M. Wang, A. Kakinen, M. Sani, M. Whittaker, E. Gurzov, F. Ding, J. Quinn, T. Davis, P. Ke, \u201cStar Polymers Reduce IAPP Toxicity via Accelerated Amyloid Aggregation\u201d, Biomacromolecules, 18 4249\u20134260, (2017) DOI: 10.1021\/acs.biomac.7b01301<\/a>
\n-Featured as ACS Editors\u2019 Choice and Journal Front Cover<\/a> Article<\/p>\n

101. Y. Sun, B. Wang, X. Ge and F. Ding, \u201cDistinct Oligomerization and Fibrillization Dynamics of Amyloid Core Sequences of Amyloid-beta and Islet Amyloid Polypeptide\u201d, Phys. Chem. Chem. Phys., 19, 28414-28423 (2017) DOI: CP\/C7CP05695H<\/a><\/p>\n

100. J. Yang, B. Wang, Y. You, W. Chang, K. Tang, Y. Wang, W. Zhang, F. Ding, S. Gunasekaran, \u201cProbing the modulated formation of gold nanoparticle-beta lactoglobulin corona complexes and its applications\u201d, Nanoscale, 9(45):17758-17769 (2017) DOI: 10.1039\/C7NR02999C <\/a>
\n-Featured as the back cover.<\/p>\n

99. B. Wang, E.H. Pilkington, Y. Sun, T.P. Davis, P.C. Ke and F. Ding, \u201cModulating protein amyloid aggregation with nanomaterials\u201d, Environmental Science Nano, 4, 1772-1783 (2017) DOI: 10.1039\/C7EN00436B<\/a><\/p>\n

98. X. Ge, A. Kakinen, E.N. Gurzov, W. Yang, L. Pang, E.H. Pilkington, P. Govindan-Nedumpully, P. Chen, F. Separovic, T.P. Davis, P. C. Ke, and F. Ding, \u201cZinc-coordination and C-peptide complexation: a potential mechanism for the endogenous inhibition of IAPP aggregation\u201d, Chem. Comm., 53(68):9394-9397 (2017) DOI: 10.1039\/C7CC04291D<\/a>
\n-Featured as the Cover article<\/a>.<\/p>\n

97. N.K. Geitner, W. Zhao, F. Ding, W. Chen, M. R. Wiesner, \u201cMechanistic Insights from Discrete Molecular Dynamics Simulations of PesticideNanoparticle Interactions\u201d, Environmental Science & Technology, 51(15):8396-8404 (2017) [link]<\/a><\/p>\n

96. P.C. Ke, M. Sani, F. Ding, A. Kakinen, I. Javed, F. Separovic, T. P. Davis, and R. Mezzenga, \u201cImplications of Peptide Assemblies in Amyloid Diseases\u201d, Chem. Soc. Rev., 46:6492-6531 (2017) [download]<\/a>
\n-Featured as the front Cover article<\/p>\n

95. S. Lin, M. Mortimer, R. Chen, A. Kakinen, J.E. Riviere, T.P. Davis, F. Ding, and P. C. Ke, \u201cNanoEHS beyond Toxicity \u2013 Focusing on Biocorona\u201d, Env. Sci. Nano, 4, 1433-1454 (2017) [link]<\/a>[download]<\/a>
\n-Featured as the Cover article.<\/p>\n

94. Pilkington E.H., Xing Y., Wang B., Kakinen A., Wang M., Davis T.P., Ding F., Ke P.C., \u201cEffects of Protein Corona on IAPP Amyloid Aggregation, Fibril Remodelling, and Cytotoxicity\u201d, Scientific Reports, 7(1):2455 (2017) [link]<\/a><\/p>\n

93. Community\/Group Publication \u2014 Miao, Z., Adamiak, R. W., Antczak, M., Batey, R. T., Becka, A. J., Biesiada, M., Boniecki, M. J., Bujnicki, J., Chen, S. J., Cheng, C. Y., Chou, F. C., Ferr\u00e9-D\u2019Amar\u00e9 A. R., Das, R., Dawson W. K., Ding, F., Dokholyan, N. V., Dunin-Horkawicz, S., Geniesse, C., Kappel, K., Kladwang, W., Krokhotin, A., Lach, G. E., Major, F., Mann, T. H., Magnus, M., Pachulska-Wieczorek, K., Patel, D. J., Piccirilli, J. A., Popenda, M., Purzycka, K. J., Ren, A., Rice, G. M., Santalcia, J. Jr., Sarzynska, J., Szachniuk, M., Tandon, A., Trausch, J. J., Tian, S., Wang, J., Weeks, K. M., Williams B. 2nd, Xiao, Y., Xu, X., Zhang, D., Zok, T., and Westhof, E. \u201cRNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme\u201d, RNA, 23(5):655-672 (2017) [link]<\/a><\/p>\n

92. B. Wang,T. Blin, A. K\u00e4kinen, X. Ge, E.H. Pilkington, J.F. Quinn, M.R. Whittaker, T.P. Davis, P.C. Ke and F. Ding, \u201cBrushed polyethylene glycol and phosphorylcholine for grafting nanoparticles against protein binding\u201d, Polymer Chemistry, 7(45):6875-6879 (2016) [link]<\/a>[Download]<\/a>
\n-Featured as the Cover article.<\/p>\n

91. E. Salonen, F. Ding, and P.C. Ke, \u201cFate, behavior and biophysical modeling of nanoparticles in living systems\u201d in \u201cEngineered Nanoparticles and the Environment: Biophysicochemical Processes and Toxicity\u201d, Edited by B. Xing, C.D. Vecitis, & N. Senesi, Wiley-IUPAC (2016) [download]<\/a><\/p>\n

90. Hadi-Alijanvand, H., Proctor, E. A., Ding, F., Dokholyan, N. V. and Moosavi-Movahedi, A. A. \u201cA Hidden Aggregation-Prone Structure in the Heart of Hypoxia Inducible Factor Prolyl Hydroxylase\u201d, Proteins: Structure, Function and Bioinformatics, 84(5): 611-623 , (2016) [link]<\/a><\/p>\n

89. T. Blin, A. Kakinen, E.H. Pilkington, A. Ivask, F. Ding, J.F. Quinn. M.R. Whittaker, P.C. Ke and T.P. Davis, \u201cSynthesis and In Vitro Properties of Iron Oxide Nanoparticles Grafted with Brushed Phosphorylcholine and Polyethylene Glycol\u201d, Polymer Chemistry, 7:1931-1944 (2016) [link]<\/a><\/p>\n

88. Nedumpully-Govindan P., Domen J., and Ding F., \u201cCSAR Benchmark of flexible MedusaDock in affinity prediction and native-like binding pose selection\u201d, Journal of Chemical Information and Modeling, 56(6): 1042-1052 (2016) [link]<\/a><\/p>\n

87. E.N. Gurzov, B. Wang, E.H. Pilkington, P. Chen,A. Kakinen, W.J. Stanley, S.A. Litwak, E.G. Hanssen,T.P. Davis, F. Ding, and P.Chun Ke, \u201cInhibition of hIAPP Amyloid Aggregation and Pancreatic \u03b2-cell Toxicity by OH-terminated PAMAM Dendrimer\u201d, Small, 12(12):1615\u20131626 (2016) [link]<\/a><\/p>\n

86. P. Nedumpully-Govindan, E.N. Gurzov, P. Chen, E.H. Pilkington, W.J. Stanley, S.A. Litwak, T.P. Davis, P.C. Ke, and F. Ding, \u201cGraphene Oxide Inhibits hIAPP Amyloid Fibrillation and Toxicity in Insulin-Producing NIT-1 Cells\u201d, Phys. Chem. Chem. Phys., 18:94-100 (2016) [download]<\/a><\/p>\n

85. P. Nedumpully-Govindan, A. Kakinen, E.H. Pilkington, T.P. Davis, P.C. Ke and F. Ding, \u201cStabilizing Off-pathway Oligomers by Polyphenol Nanoassemblies for IAPP Aggregation Inhibition\u201d, Scientific Reports 6: 19463 (2016) [download]<\/a><\/p>\n

84. S. Radic, T.P. Davis, P.C. Ke and F. Ding, \u201cContrasting effects of nanoparticle-protein attraction on amyloid aggregation\u201d, RSC Advances, 5, 105489-105498 (2015)[download]<\/a><\/p>\n

83. P. Nedumpully-Govindan, Y. Yang, R. Andorfer, W. Cao, and F. Ding, \u201cPromotion or Inhibition of IAPP Aggregation by Zinc Coordination Depends on Its Relative Concentration\u201d, Biochemistry, 54:7335-44 (2015)[download]<\/a><\/p>\n

82. Wang B, Geitner NK, Davis TP, Ke PC, Ladner DL and Ding F, \u201cDeviation from the Unimolecular Micelle Paradigm of PAMAM Dendrimers Induced by Strong Inter-Ligand Interactions\u201d, Journal of Physical Chemistry C, 119, 19475\u201319484 (2015) [download]<\/a><\/p>\n

81. Ge XW, Ke PC, Davis TP and Ding F, \u201cA Thermodynamics Model for the Emergence of a Stripe-like Binary SAM on a Nanoparticle Surface\u201d, Small 11(37):4894\u20134899 (2015) [link]<\/a>
\n-Featured as the Cover article [link]<\/a><\/p>\n

80. Community\/Group Publication \u2014 Miao Z, Adamiak RW, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cheng C, Chojnowski G, Chou FC, Cordero P, Cruz JA, Ferr\u00e9-D\u2019amar\u00e9 AR, Das R, Ding F, Dokholyan NV, Dunin-Horkawicz S, Kladwang W, Krokhotin A, Lach G, Magnus M, Major F, Mann TH, Masquida B, Matelska D, Meyer M, Peselis A, Popenda M, Purzycka KJ, Serganov A, Stasiewicz J, Szachniuk M, Tandon A, Tian S, Wang J, Xiao Y, Xu X, Zhang J, Zhao P, Zok T, Westhof E., \u201cRNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures\u201d, RNA, 21(6):1066-84. (2015) [download]<\/a><\/p>\n

79. DeFever R., Geitner N., Bhattacharya P., Ding F., Ke P.C., Sarupria S., \u201cPAMAM dendrimers and graphene: Materials for removing aromatic contaminants from water\u201d, Environmental Science & Technology, 49:4490-7 (2015) [download]<\/a><\/p>\n

78. Nedumpully-Govindan P. and Ding F., \u201cInhibition of IAPP aggregation by insulin depends on the insulin oligomeric state regulated by zinc ion concentration\u201d, Scientific Reports 5, (2015) [download]<\/a><\/p>\n

77. Wang B., Seabrook S.A., Nedumpully-Govindan P., Chen P., Yin H., Waddington L., Epa V.C., Winkler D.A., Kirby J.K., Ding F., Ke P.C., \u201cThermostability and Reversibility of Silver Nanoparticle-Protein Binding\u201d, Physical Chemistry Chemical Physics, 17:1728-1739 (2015) [download]<\/a><\/p>\n

76. Geitner N., Wang B., Andorfer R.; Ladner D.; Ke P.K.; Ding F., \u201cThe structure-function relationship of PAMAM dendrimers as robust oil dispersants\u201d, Environmental Science & Technology, 48(21):12868-75, (2014) [download]<\/a><\/p>\n

75. Homan, P., Tandon, A., Rice, G. M., Ding, F., Dokholyan, N. V., and Weeks, K. M. \u201cRNA tertiary structure analysis and refinement by 2\u2032-hydroxyl molecular interference\u201d, Biochemistry, 53(43):6825-33 (2014) [download]<\/a><\/p>\n

74. S. Radic, P. Nedumpully-Govindan,R. Chen, E. Salonen, J.M. Brown, P.C. Ke, and F. Ding, \u201cEffect of Fullerenol Surface Chemistry on Nanoparticle Binding-induced Protein Misfolding\u201d, Nanoscale, 6 (14), 8340 \u2013 8349 (2014) [download]<\/a><\/p>\n

73. P. Nedumpully-Govindan, L. Li, E.G. Alexov, M.A. Blenner, and F. Ding, \u201cStructural and energetic determinants of tyrosylprotein sulfotransferase sulfation specificity\u201d, Bioinformatics, 30(16):2302-9 (2014) [download]<\/a><\/p>\n

72. P. Toran, I. Smolina, H. Driscoll,F. Ding, Y.J. Sun, C.R. Cantor, and N. Broude, \u201cLabeling native bacterial RNA in live cells\u201d, Cell Research, 24(7):894-7 (2014) [download]<\/a><\/p>\n

71. Redler, R.L., Shirvanyants, D., Dagliyan, O., Ding, F., Kim, D.N., Kota, P., Proctor, E.A., Ramachandran, S., Tandon, A., and Dokholyan, N.V. \u201cComputational approaches to understanding protein aggregation in neurodegeneration.\u201d, Journal of Molecular Cell Biology, 6(2):104-15 (2014) [download]<\/a><\/p>\n

70. Y. Wen, N.K. Geitner, R. Chen, F. Ding, P. Chen, R.E. Andorfer, P.N. Govindan, and P.C. Ke, Binding of Cytoskeletal Proteins with Silver Nanoparticles, RSC Advances, 3: 22002-22007, (2013)[download]<\/a><\/p>\n

69. A. Kakinen, F. Ding, P. Chen, M. Mortimer, A. Kahru, and P.C. Ke, \u201cInteraction of Silver Nanoparticles and Firefly Luciferase and Its Impact on Enzyme Activity\u201d, Nanotechnology, 24: 345101 (2013)[download]<\/a><\/p>\n

68. F. Ding*, S. Radic, N. Geitner, R. Chen, P. Chen, J.M. Brown and P.C. Ke*, \u201cDirect observation of silver nanoparticle-ubiquitin corona formation\u201d, Nanoscale, online 16 Jul 2013 (2013)[download]<\/a><\/p>\n

67. S. Radic, N. Geitner, R. Podila, A. Kakinen, P. Chen, P.C. Ke, and F. Ding, \u201cCompetitive Binding of Natural Amphiphiles with Graphene Derivatives\u201d, Scientific Reports, on line 24 July (2013) [download]<\/a><\/p>\n

66. Fourche, D., Muratov, E., Ding, F., Dokholyan, N. V., Tropsha, A. \u201cPredicting binding affinity of CSAR ligands using both structure-based and ligand-based approaches\u201d, Journal of Chemical Information and Modeling, 53: 1915\u20131922 (2013)[download]<\/a><\/p>\n

65. N. E. Hudson, F. Ding, I. Bucay, E. T. O\u2019Brien III, O. V. Gorkun, R. Superfine, S. T. Lord, N. V. Dokholyan, and M. R. Falvo, \u201cSubmillisecond Elastic Recoil Reveals Molecular Origins of Fibrin Fiber Mechanics\u201d Biophysical Journal, 104:2671\u20132680 (2013)[download]<\/a><\/p>\n

64. Dagliyan, O., D. Shirvanyants, A. Karginov, F. Ding, L. Fee, S.N. Chandrasekaran, C.M Freisinger, G. Smolen, A. Huttenlocher, K. M. Hahn, & N. V. Dokholyan, \u201cRational design of a ligand-controlled protein conformational switch\u201d, Proceedings of the National Academy of Sciences USA, 119(17):6800-6804 (2013)[download]<\/a><\/p>\n

63. Ramachandran, S.*, Ding, F.*, Weeks, K., and Dokholyan, N. V. \u201cStatistical analysis of SHAPE-directed RNA secondary structure modeling\u201d, Biochemistry, 52:596-599 (2013)[download]<\/a><\/p>\n

62. F. Ding and N.V. Dokholyan, \u201cIncorporating backbone flexibility in MedusaDock improves ligand binding pose prediction in the CSAR2011 docking benchmark\u201d, J. Chem. Inf. Model., 53:1871-1879 (2013) [download]<\/a><\/p>\n

61. D.I. Cole, J.D. Legassie, L.N. Bonifacio, V.G. Sekaran, F. Ding, N.V.  Dokholyan & M. B. Jarstfer, \u201cNew Models of Tetrahymena Telomerase RNA from Experimen- tally Derived Constraints and Modeling\u201d, JACS, 34: 20070\u201320080 (2012)[download]<\/a><\/p>\n

60. F. Ding. and Dokholyan, N. V., \u201cRNA three-dimensional structure determination using experimental constraints\u201d, in \u201cRNA Nanotechnology and Therapeutics\u201d edited by Dr. Peixuan Guo, pp 159-176, (2012)[download]<\/a><\/p>\n

59. Sparta, M., Shirvanyants, D., F., Ding, Dokholyan, N. V., and Alexandrova, A. N. \u201cHybrid dynamics simulation engine for metalloproteins\u201d, Biophysical Journal, 103:767-776 (2012)[download]<\/a><\/p>\n

58. F. Ding, C. Lavendar, K.M. Weeks, and N.V. Dokholyan, \u201cThree-Dimensional RNA Structure Refinement by Hydroxyl Radical Probing\u201d, Nature Methods, 9(6):603-608 (2012)[download]<\/a>
\n*Accompanied by a news and review paper: Behrouzi, R. and Woodson, S.R., \u201cRendering RNA in 3D\u201d, Nature Methods, 9(6):552-3 (2012)[link]<\/a><\/p>\n

57. F. Ding, Y. Furukawa, N. Nukina, and Dokholyan, N.V., \u201cLocal unfolding of Cu, Zn superoxide Dismutase monomer determines the morphology of fibrillar aggregates\u201d, Journal of Molecular Biology, 421:548-560 (2012)[download]<\/a><\/p>\n

56. F. Ding, and Dokholyan, N.V. \u201cDiscrete molecular dynamics simulation of biomolecules.\u201d in \u201cComputational Modeling of Biological Systems: From Molecules to Pathways\u201d, E. Springer, (2012) [download]<\/a><\/p>\n

55. F. Ding and Dokholyan N.V., \u201cMultiscale modeling of RNA Structure and Dynamics\u201d in \u201cRNA 3D Structure Analysis and Prediction\u201d, Edited by Leontis, N. and Westhof, E. Springer, 2012 [download]<\/a><\/p>\n

54. Nakayama, T., Butler, J. S., Sehgal, A., Severgnini, M., Racie, T., Sharman J., F. Ding, Morskaya, S. S., Brodsky, J., Tchangov, L., Kosovrasti, V., Meys, M., Nechev, L., Wang, G., Peng, C. G., Fang, Y., Maier, M., Rajeev, K. G., Li, R., Hettinger, J., Barros, S., Clausen, V., Zhang, X., Wang, Q., Hutabarat, R., Dokholyan, N. V., Wolfrum, C., Manoharan, M., Kotelianski, V., Stoffel, M. and Sah, D. W. Y. \u201cHarnessing a Physiologic Mechanism for siRNA Delivery with Mimetic Lipoprotein Particles\u201d, Molecular Therapy, 20:1582-9, (2012) [download]<\/a>(2012)<\/p>\n

53. Community\/Group Publication \u2014 Cruz, J. A., Blanchet, M-F., Boniecki, M., Bujnicki, J. M., Chen, S-J., Cao, S., Das, R., F. Ding, Dokholyan, N. V., Flores, S. C., Lavender C. A., Lisi, V., Major, F., Mikolajczak, K., Philips, A., Puton, T., Santalucia, J., Siyenji, F., Hermann, T., Rother, K., Rother, M., Serganov, S., Skorupski, M., Soltysinski, T., Sripakdeevong, P., Tuszynska, I., Weeks, K. M., Waldsich, C., Wildauer, M., Leontis, N. B. and Westhof, E. \u201cRNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction\u201d, RNA, 18:610-625 [download]<\/a> (2012)<\/p>\n

52. Shirvanyants, D., F. Ding, Tsao, D., Ramachandran, S. and Dokholyan, N. V. \u201cDMD: an efficient and versatile simulation method for fine protein characterization\u201d, Journal of Physical Chemistry B, 116:8375-82 [download]<\/a> (2012)<\/p>\n

51. Dagliyan, O., Proctor, E. A., D\u2019Auria, K., F. Ding* and Dokholyan N. V.* \u201cStructural and Dynamic Determinants of Protein-peptide Recognition\u201d, Structure, 19:1837 (2011) [download]<\/a>
\n*Featured in the Journal Cover of Structure.<\/p>\n

50. A.W.R. Serohijos, S. Yin, F. Ding, J. Gauthier, D.G. Gibson, V. Setola, W. Maixner, Dokholyan, N.V., and L. Diatchenko, \u201cStructural basis for MOR1 binding and activation\u201d, Structure, 19:1683-1690 (2011) [download]<\/a><\/p>\n

49. Kota, P.*, F. Ding*, Ramachandran, S.*, and Dokholyan, N.V. \u201cGaia: automated structure quality assessment of protein models\u201d, Bioinformatics, 27:2209-2215 (2011) [download]<\/a>[service]<\/a><\/p>\n

48. Proctor, E. A., F. Ding, and Dokholyan, N. V. \u201cStructural and thermodynamic effects of post-translational modifications in mutant and wild type Cu, Zn superoxide dismutase\u201d, Journal of Molecular Biology, 408:555-567 (2011). [download]<\/a><\/p>\n

47. Ramachandran, S., Kota, P., F. Ding and Dokholyan, N. V. \u201cAutomated Minimization of Steric Clashes in Protein Structures\u201d, Proteins: Structure, Function and Bioinformatics, 79:261-270 (2011)[download]<\/a>[service]<\/a><\/p>\n

46. F. Ding, Yin, S., and Dokholyan, N. V. \u201cRapid flexible docking using a stochastic rotamer library of ligands\u201d, Journal of Chemical Information and Modeling, 50:1623-32 (2010) [download]<\/a><\/p>\n

45. A. Karginov, F. Ding, P. Kota, Dokholyan, N.V. and K. Hahn, \u201cEngineered allosteric regulation of kinases in living cells\u201d, Nature Biotechnology, 28:743-748, (2010) [download]<\/a><\/p>\n

44. C. Lavender, F. Ding, Dokholyan, N.V., K.M. Weeks, \u201cRobust and Generic RNA Modeling Using Inferred Constraints: A Structure for the Hepatitis C Virus IRES Pseudoknot Domain, Biochemistry, 49:4931-4933 (2010)[download]<\/a><\/p>\n

43. E.A. Proctor, F. Ding, and Dokholyan, N.V., \u201cDiscrete Molecular Dynamics\u201d, Wiley Interdisciplinary Reviews: Computational Molecular Science, 1:80-92 (2010)[download]<\/a><\/p>\n

42. V. V. Lakhani, F. Ding and N. V. Dokholyan, \u201cPoly-glutamine induced misfolding of huntingtin exon1 is modulated by the flanking sequences\u201d Public Library of Science Computational Biology:e1000772 (2010)[download]<\/a><\/p>\n

41. C. Hajdin, F. Ding, N. V. Dokholyan, and K. M. Weeks, \u201cHow good is that RNA tertiary structure prediction?\u201d RNA, 16:1340-1349 (2010) [download]<\/a> [service]<\/a><\/p>\n

40. B. A. Kesner, F. Ding, B. S. Temple, and N. V. Dokholyan, \u201cN-terminal strands of filamin Ig domains act as a conformational switch under biological forces\u201d Proteins: Structure, Function, and Bioinformatics, 78:12-24 (2009)[download]<\/a><\/p>\n

39. M. P. Torres, M. J. Lee, F. Ding, C. Purbeck, B. Kuhlman, N. V. Dokholyan, and H. G. Dohlman, \u201cG Protein Mono-Ubiquitination By the RSP5 Ubiquitin Ligase\u201d, Journal of Biological Chemistry, 284: 8940-8950 (2009)[download]<\/a><\/p>\n

38. Yin, S., F. Ding and Dokholyan, N. V. \u201cModeling mutations in proteins using Medusa and discrete molecular dynamics\u201d in \u201cProtein Structure Prediction: Method and Algorithms\u201d, Editors: Rangwala, H. and Karypis, G. Wiley & Sons, (2009)<\/p>\n

37. S. Yin, F. Ding, and N. V. Dokholyan, \u201cComputational evaluation of protein stability change upon mutations using Eris.\u201d in \u201cIn Vitro Mutagenesis Protocols\u201d Editor: J. Braman. Humana Press (2009)<\/p>\n

36. C. M. Gherghe, C. W. Leonard, F. Ding, N. V. Dokholyan, and K. M. Weeks, \u201cNative-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics\u201d Journal of the American Chemical Society , 131:2541-2546(2009) [download]<\/a><\/p>\n

35. F. Ding and N. V. Dokholyan, \u201cDynamical roles of metal ions and the disulfide bond in Cu, Zn superoxide dismutase folding and aggregation\u201d Proceedings of the National Academy of Sciences USA, 105:19696-19701 (2008) [download]<\/a><\/p>\n

34. S. Sharma, F. Ding, and N. V. Dokholyan, \u201ciFoldRNA: Three-dimensional RNA structure prediction and folding\u201d Bioinformatics, 24:1951-1952 (2008) [download]<\/a> [service]<\/a><\/p>\n

33. D. G. Teotico, M. Frazier, F. Ding, N. V. Dokholyan, B. Temple, and M. R. Redinbo, \u201cActive nuclear receptors exhibit highly correlated AF-2 domain motions\u201d Public Library of Science Computational Biology, 4: e1000111 (2008) [download]<\/a><\/p>\n

32. F. Ding, D. Tsao, H. Nie, and N. V. Dokholyan, \u201cAb initio folding of proteins using all-atom discrete molecular dynamics\u201d Structure, 16: 1010-1018 (2008) [download]<\/a><\/p>\n

31. F. Ding, S. Sharma, P. Chalasani, V. V. Demidov, N. E. Broude, and N. V. Dokholyan, \u201cLarge scale simulations of 3D RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms\u201d RNA, 14: (2008) [download]<\/a><\/p>\n

30. S. Sharma, F. Ding, and N. V. Dokholyan, \u201cProbing protein aggregation using simplified models and discrete molecular dynamics\u201d Frontiers in Bioscience, 13: 4795-4808 (2008) [download]<\/a><\/p>\n

29. S. Yin, F. Ding, and N. V. Dokholyan, \u201cModeling backbone flexibility improves protein stability estimation\u201d, Structure, 15: 1567-1576 (2007) [download]<\/a><\/p>\n

28. A. R. Lam, J. M. Borreguero, F. Ding, N. V. Dokholyan, S. V. Buldyrev, E. I. Shakhnovich, H. E. Stanley, \u201cParallel folding pathways in the Src SH3 domain\u201d Journal of Molecular Biology, 373: 1348-1360 (2007) [download]<\/a><\/p>\n

27. S. Barton, R. Jacak, S. D. Khare, F. Ding*, and N. V. Dokholyan*, \u201cThe length dependence of the polyQ-mediated protein aggregation\u201d Journal of Biological Chemistry, 282: 25487-25492 (2007) [download]<\/a><\/p>\n

26. Y. Chen, F. Ding, H. Nie, A. W. Serohijos, S. Sharma, K. C. Wilcox, S. Yin, and N. V. Dokholyan, \u201cProtein folding: then and now\u201d Archives of Biochemistry and Biophysics, 469: 4-19 (2008) [download]<\/a><\/p>\n

25. S. Yin, F. Ding, and N. V. Dokholyan, \u201cEris: An automated estimator of protein stability\u201d Nature Methods, 4: 466-467 (2007) [download]<\/a>[service]<\/a><\/p>\n

24. Y. Chen, F. Ding, and N. V. Dokholyan, \u201cFidelity of protein structure reconstruction from inter-residue proximity constraints\u201d Journal of Physical Chemistry B, 111: 7432-7438 (2007) [download]<\/a><\/p>\n

23. S. Sharma, F. Ding, and N. V. Dokholyan, \u201cMulti-scale modeling of nucleosome dynamics\u201d Biophysical Journal, 92 1457-1470 (2007) [download]<\/a><\/p>\n

22. A. W. Serohijos, Y. Chen, F. Ding, T. C. Elston, and N. V. Dokholyan, \u201cA new structural model reveals energy transduction in dynein\u201d, Proceedings of the National Academy of Sciences USA, 103: 18540-18545 (2006)[download]<\/a><\/p>\n

21. S. Sharma, F. Ding, H. Nie, D. Watson, A. Unnithan, J. Lopp, D. Pozefsky, and N. V. Dokholyan, \u201ciFold: A platform for interactive folding simulations of proteins\u201d Bioinformatics, 22: 2693-2694 (2006) [download]<\/a>[service]<\/a><\/p>\n

20. F. Ding and N. V. Dokholyan, \u201cEmergence of protein fold families through rational design\u201d Public Library of Science Computational Biology, 2: e85 (2006) [download]<\/a><\/p>\n

19. V. V. Demidov, N. V. Dokholyan, C. Witte-Hoffman, P. Chalasani, H.-W. Yiu, F. Ding, Y. Yu, C. R. Cantor, N. E. Broude, \u201cFast complementation of split fluorescent protein triggered by DNA hybridization\u201d, Proceedings of the National Academy of Sciences USA, 103: 2052-2056 (2006). [download]<\/a><\/p>\n

18. F. Ding, J. J. LaRocque, and N. V. Dokholyan, \u201cDirect observation of protein folding, aggregation and a prion-like conformational transition\u201d, Journal of Biological Chemistry, 280: 40235-40240 (2005) [download]<\/a><\/p>\n

17. F. Ding, K. C. Prutzman, S. L. Campbell, and N. V. Dokholyan, \u201cTopological determinants of protein domain swapping\u201d, Structure, 14: 5-14 (2005). [download]<\/a>[service]<\/a><\/p>\n

16. S. D. Khare, F. Ding, K. N. Gwanmesia, and N. V. Dokholyan, \u201cMolecular origin of polyglutamine-mediated protein aggregation in neurodegenerative diseases\u201d, PLoS Computational Biology, 1, e30 (2005). [download]<\/a><\/p>\n

15. F. Ding, W. Guo, N. V. Dokholyan, E. I. Shakhnovich, and J.-E. Shea, \u201cReconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations\u201d, J. Mol. Biol., 350: 1035-1050 (2005). [download]<\/a><\/p>\n

14. F. Ding and N. V. Dokholyan, \u201cSimple but predictive protein models\u201d, Trends in Biotechnology, 23: 450-455 (2005). [download]<\/a><\/p>\n

13. F. Ding, R. K. Jha, and N. V. Dokholyan, \u201cScaling behavior and structure of denatured proteins\u201d, Structure, 13: 1047-1054 (2005). [download]<\/a>
\n-Featured as Journal Front Cover<\/p>\n

12. F. Ding, S. V. Buldyrev, and N. V. Dokholyan, \u201cFolding Trp-cage to NMR resolution native structure using a coarse-grained protein model\u201d, Biophys. J., 88: 147-155 (2005). [download]<\/a><\/p>\n

11. R. D. S. Dixon, Y. Chen, F. Ding, S. D. Khare, K. C. Prutzman, M. D. Schaller, S. L. Campbell, and N. V. Dokholyan, \u201cNew insights into FAK signaling and localization based on detection of a FAT domain folding intermediate\u201d Structure, 12: 2161-2171 (2004). [download]<\/a><\/p>\n

10. B. Urbanc, L. Cruz, F. Ding, D. Sammond, S. Khare, S. V. Buldyrev, H. E. Stanley, and N. V. Dokholyan, \u201cMolecular dynamics simulation of Amyloid beta dimer formation\u201d Biophys. J., 87: 2310-2321 (2004). [download]<\/a><\/p>\n

9. J. M. Borreguero, F. Ding, S. V. Buldyrev, H. E. Stanley, and N. V. Dokholyan, \u201cMultiple folding pathways of the SH3 domain.\u201d Biophys. J. 87: 521-533 (2004). [download]<\/a><\/p>\n

8. S. Peng, F. Ding, B. Urbanc, S. V. Buldyrev, L. Cruz , H. E. Stanley, and N. V. Dokholyan, \u201cDiscrete molecular dynamics simulations of peptide aggregation\u201d Phys. Rev. E 69: 041908 (2004) [download]<\/a><\/p>\n

7. S. D. Khare, F. Ding and N. V. Dokholyan, \u201cFolding of Cu,Zn superoxide dismutase and Familial Amyotrophic Lateral Sclerosis.\u201d J. Mol. Biol, 334, 515-525, 2003 [download]<\/a><\/p>\n

6. Dokholyan N.V., Borreguero J.M., Buldyrev S.V., F. Ding, Stanley H.E. and Shakhnovich E.I., Identifying the importance of amino acids for protein folding from crystal structures, Methods in Enzymology Vol. 374: pp 618-640 Macromolecular crystallography D. Editors: C. W. Carter Jr. and R. M. Sweet (2003) [download]<\/a><\/p>\n

5. F. Ding, Borreguero J.M., Buldyrev S.V., Stangley H.E. and Dokholyan N.V., A mechanism for alpha-helix to beta-hairpin transition, Proteins: Structure, Function and Genetics, 53:220-228 (2003) [download]<\/a><\/p>\n

4. F. Ding, Dokholyan N.V., Buldyrev S.V., Stanley H.E. and Shakhnovich E.I., Molecular dynamics simulation of C-Src SH3 aggregation suggests a generic amyloidogenesis mechanism, J Mol Biol, 324:851-857 2002 [download]<\/a><\/p>\n

3. Dokholyan N.V., Li L., Ding F., Shakhnovich E.I., Topological determinants of protein folding, Proceedings of the National Academy of Sciences USA,, 99 (13): 8637-8641 JUN 25 2002 [download]<\/a><\/p>\n

2. F. Ding, Dokholyan V.N., Buldyrev V.S., Stanley H.E. and Shakhnovich E.I. Direct molecular dynamics observation of protein folding transition state ensemble. Biophys J., 86 (6): December 2002 [download]<\/a><\/p>\n

1. X.Y. Lei, H. Li, F. Ding, W. Zhang, and N.B. Ming, Novel application of a perturbed photonic crystal: High-quality filter. APPL PHYS LETT 71 (20): 2889-2891 NOV 17 1997 [download]<\/a><\/p>\n

\n","protected":false},"excerpt":{"rendered":"

External publication lists: Pubmed, Google Scholar, Web of Science 207. Y. Sun, N. Andrikopoulos, F. Ding*, P.C. Ke*, “An endogenous beta-endorphin corona confers neuroprotection against Alzheimer’s amyloidogenesis”, Neural Regeneration Research (2026) doi: 10.4103\/NRR.NRR-D-25-01700 206. S. Wu, L. Zhou, X. Kang, G. Huang, Y. Cha, J. Shen, C. Wang, K. H. Lackey, D. Kim, F. Ding*, … <\/p>\n

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