Publications

Google scholar profile: Feng Ding

Researcherid: G-6029-2011

PubMed: PubMed List


 

100. J. Yang, B. Wang, Y. You, W. Chang, K. Tang, Y. Wang, W. Zhang, F. Ding, S. Gunasekaran, “Probing the modulated formation of gold nanoparticle-beta lactoglobulin corona complexes and its applications”, Nanoscale, in press (2017) [link]

99. B. Wang, E.H. Pilkington, Y. Sun, T.P. Davis, P.C. Ke and F. Ding, “Modulating protein amyloid aggregation with nanomaterials”, Environmental Science Nano, in press (2017) [link]

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, “Zinc-coordination and C-peptide complexation: a potential mechanism for the endogenous inhibition of IAPP aggregation”, Chem. Comm., in press (2017) [link]
-Featured as the Cover article.

97. N.K. Geitner, W. Zhao, F. Ding, W. Chen, M. R. Wiesner, “Mechanistic Insights from Discrete Molecular Dynamics Simulations of PesticideNanoparticle Interactions”, Environmental Science & Technology, in press (2017) [link]

96. P.C. Ke, M. Sani, F. Ding, A. Kakinen, I. Javed, F. Separovic, T. P. Davis, and R. Mezzenga, “Implications of Peptide Assemblies in Amyloid Diseases”, Chem. Soc. Rev., in press (2017) [download]

95. S. Lin, M. Mortimer, R. Chen, A. Kakinen, J.E. Riviere, T.P. Davis, F. Ding, and P. C. Ke, “NanoEHS beyond Toxicity – Focusing on Biocorona”, Env. Sci. Nano, 4, 1433-1454 (2017) [link][download]
-Featured as the Cover article.

94. Pilkington E.H., Xing Y., Wang B., Kakinen A., Wang M., Davis T.P., Ding F., Ke P.C., “Effects of Protein Corona on IAPP Amyloid Aggregation, Fibril Remodelling, and Cytotoxicity”, Scientific Reports, in press (2017) [link]

93. 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., Ferré-D’Amaré 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. “RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme”, RNA, in press (2017) [link]

92. B. Wang,T. Blin, A. Käkinen, X. Ge, E.H. Pilkington, J.F. Quinn, M.R. Whittaker, T.P. Davis, P.C. Ke and F. Ding, “Brushed polyethylene glycol and phosphorylcholine for grafting nanoparticles against protein binding”, Polymer Chemistry, in press (2016) [link][Download]
-Featured as the Cover article.

91. E. Salonen, F. Ding, and P.C. Ke, “Fate, behavior and biophysical modeling of nanoparticles in living systems” in “Engineered Nanoparticles and the Environment: Biophysicochemical Processes and Toxicity”, Edited by B. Xing, C.D. Vecitis, & N. Senesi, Wiley-IUPAC (2016) [download]

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

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, “Synthesis and In Vitro Properties of Iron Oxide Nanoparticles Grafted with Brushed Phosphorylcholine and Polyethylene Glycol”, Polymer Chemistry, 7:1931-1944 (2016) [link]

88. Nedumpully-Govindan P., Domen J., and Ding F., “CSAR Benchmark of flexible MedusaDock in affinity prediction and native-like binding pose selection”, Journal of Chemical Information and Modeling, 56(6): 1042-1052 (2016) [link]

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, “Inhibition of hIAPP Amyloid Aggregation and Pancreatic β-cell Toxicity by OH-terminated PAMAM Dendrimer”, Small, 12(12):1615–1626 (2016) [link]

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, “Graphene Oxide Inhibits hIAPP Amyloid Fibrillation and Toxicity in Insulin-Producing NIT-1 Cells”, PCCP, 18:94-100 (2016) [download]

85. P. Nedumpully-Govindan, A. Kakinen, E.H. Pilkington, T.P. Davis, P.C. Ke and F. Ding, “Stabilizing Off-pathway Oligomers by Polyphenol Nanoassemblies for IAPP Aggregation Inhibition”, Scientific Reports 6: 19463 (2016) [download]

84. S. Radic, T.P. Davis, P.C. Ke and F. Ding, “Contrasting effects of nanoparticle-protein attraction on amyloid aggregation”, RSC Advances, 5, 105489-105498 (2015)[download]

83. P. Nedumpully-Govindan, Y. Yang, R. Andorfer, W. Cao, and F. Ding, “Promotion or Inhibition of IAPP Aggregation by Zinc Coordination Depends on Its Relative Concentration”, Biochemistry, 54:7335-44 (2015)[download]

82. Wang B, Geitner NK, Davis TP, Ke PC, Ladner DL and Ding F, “Deviation from the Unimolecular Micelle Paradigm of PAMAM Dendrimers Induced by Strong Inter-Ligand Interactions”, Journal of Physical Chemistry C, 119, 19475–19484 (2015) [download]

81. Ge XW, Ke PC, Davis TP and Ding F, “A Thermodynamics Model for the Emergence of a Stripe-like Binary SAM on a Nanoparticle Surface”, Small 11(37):4894–4899 (2015) [link]
-Featured as the Cover article [link]

80. Miao Z, Adamiak RW, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cheng C, Chojnowski G, Chou FC, Cordero P, Cruz JA, Ferré-D’amaré 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., “RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures”, RNA, 21(6):1066-84. (2015) [download]

79. DeFever R., Geitner N., Bhattacharya P., Ding F., Ke P.C., Sarupria S., “PAMAM dendrimers and graphene: Materials for removing aromatic contaminants from water”, Environmental Science & Technology, 49:4490-7 (2015) [download]

78. Nedumpully-Govindan P. and Ding F., “Inhibition of IAPP aggregation by insulin depends on the insulin oligomeric state regulated by zinc ion concentration”, Scientific Reports 5, (2015) [download]

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., “Thermostability and Reversibility of Silver Nanoparticle-Protein Binding”, Physical Chemistry Chemical Physics, 17:1728-1739 (2015) [download]

76. Geitner N., Wang B., Andorfer R.; Ladner D.; Ke P.K.; Ding F., “The structure-function relationship of PAMAM dendrimers as robust oil dispersants”, Environmental Science & Technology, 48(21):12868-75, (2014) [download]

75. Homan, P., Tandon, A., Rice, G. M., Ding, F., Dokholyan, N. V., and Weeks, K. M. “RNA tertiary structure analysis and refinement by 2′-hydroxyl molecular interference”, Biochemistry, 53(43):6825-33 (2014) [download]

74. S. Radic, P. Nedumpully-Govindan,R. Chen, E. Salonen, J.M. Brown, P.C. Ke, and F. Ding, “Effect of Fullerenol Surface Chemistry on Nanoparticle Binding-induced Protein Misfolding”, Nanoscale, 6 (14), 8340 – 8349 (2014) [download]

73. P. Nedumpully-Govindan, L. Li, E.G. Alexov, M.A. Blenner, and F. Ding, “Structural and energetic determinants of tyrosylprotein sulfotransferase sulfation specificity”, Bioinformatics, 30(16):2302-9 (2014) [download]

72. P. Toran, I. Smolina, H. Driscoll,F. Ding, Y.J. Sun, C.R. Cantor, and N. Broude, “Labeling native bacterial RNA in live cells”, Cell Research, 24(7):894-7 (2014) [download]

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. “Computational approaches to understanding protein aggregation in neurodegeneration.”, Journal of Molecular Cell Biology, 6(2):104-15 (2014) [download]

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]

69. A. Kakinen, F. Ding, P. Chen, M. Mortimer, A. Kahru, and P.C. Ke, “Interaction of Silver Nanoparticles and Firefly Luciferase and Its Impact on Enzyme Activity”, Nanotechnology, 24: 345101 (2013)[download]

68. F. Ding*, S. Radic, N. Geitner, R. Chen, P. Chen, J.M. Brown and P.C. Ke*, “Direct observation of silver nanoparticle-ubiquitin corona formation”, Nanoscale, online 16 Jul 2013 (2013)[download]

67. S. Radic, N. Geitner, R. Podila, A. Kakinen, P. Chen, P.C. Ke, and F. Ding, “Competitive Binding of Natural Amphiphiles with Graphene Derivatives”, Scientific Reports, on line 24 July (2013) [download]

66. Fourche, D., Muratov, E., Ding, F., Dokholyan, N. V., Tropsha, A. “Predicting binding affinity of CSAR ligands using both structure-based and ligand-based approaches”, Journal of Chemical Information and Modeling, 53: 1915–1922 (2013)[download]

65. N. E. Hudson, F. Ding, I. Bucay, E. T. O’Brien III, O. V. Gorkun, R. Superfine, S. T. Lord, N. V. Dokholyan, and M. R. Falvo, “Submillisecond Elastic Recoil Reveals Molecular Origins of Fibrin Fiber Mechanics” Biophysical Journal, 104:2671–2680 (2013)[download]

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, “Rational design of a ligand-controlled protein conformational switch”, Proceedings of the National Academy of Sciences USA, 119(17):6800-6804 (2013)[download]

63. Ramachandran, S.*, Ding, F.*, Weeks, K., and Dokholyan, N. V. “Statistical analysis of SHAPE-directed RNA secondary structure modeling”, Biochemistry, 52:596-599 (2013)[download]

62. F. Ding and N.V. Dokholyan, “Incorporating backbone flexibility in MedusaDock improves ligand binding pose prediction in the CSAR2011 docking benchmark”, J. Chem. Inf. Model., 53:1871-1879 (2013) [download]

61. D.I. Cole, J.D. Legassie, L.N. Bonifacio, V.G. Sekaran, F. Ding, N.V.  Dokholyan & M. B. Jarstfer, “New Models of Tetrahymena Telomerase RNA from Experimen- tally Derived Constraints and Modeling”, JACS, 34: 20070–20080 (2012)[download]

60. F. Ding. and Dokholyan, N. V., “RNA three-dimensional structure determination using experimental constraints”, in “RNA Nanotechnology and Therapeutics” edited by Dr. Peixuan Guo, pp 159-176, (2012)[download]

59. Sparta, M., Shirvanyants, D., F., Ding, Dokholyan, N. V., and Alexandrova, A. N. “Hybrid dynamics simulation engine for metalloproteins”, Biophysical Journal, 103:767-776 (2012)[download]

58. F. Ding, C. Lavendar, K.M. Weeks, and N.V. Dokholyan, “Three-Dimensional RNA Structure Refinement by Hydroxyl Radical Probing”, Nature Methods, 9(6):603-608 (2012)[download]
*Accompanied by a news and review paper: Behrouzi, R. and Woodson, S.R., “Rendering RNA in 3D”, Nature Methods, 9(6):552-3 (2012)[link]

57. F. Ding, Y. Furukawa, N. Nukina, and Dokholyan, N.V., “Local unfolding of Cu, Zn superoxide Dismutase monomer determines the morphology of fibrillar aggregates”, Journal of Molecular Biology, 421:548-560 (2012)[download]

56. F. Ding, and Dokholyan, N.V. “Discrete molecular dynamics simulation of biomolecules.” in “Computational Modeling of Biological Systems: From Molecules to Pathways”, E. Springer, (2012) [download]

55. F. Ding and Dokholyan N.V., “Multiscale modeling of RNA Structure and Dynamics” in “RNA 3D Structure Analysis and Prediction”, Edited by Leontis, N. and Westhof, E. Springer, 2012 [download]

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. “Harnessing a Physiologic Mechanism for siRNA Delivery with Mimetic Lipoprotein Particles”, Molecular Therapy, 20:1582-9, (2012) [download](2012)

53. 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. “RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction”, RNA, 18:610-625 [download] (2012)

52. Shirvanyants, D., F. Ding, Tsao, D., Ramachandran, S. and Dokholyan, N. V. “DMD: an efficient and versatile simulation method for fine protein characterization”, Journal of Physical Chemistry B, 116:8375-82 [download] (2012)

51. Dagliyan, O., Proctor, E. A., D’Auria, K., F. Ding* and Dokholyan N. V.* “Structural and Dynamic Determinants of Protein-peptide Recognition”, Structure, 19:1837 (2011) [download]
*Featured in the Journal Cover of Structure.

50. A.W.R. Serohijos, S. Yin, F. Ding, J. Gauthier, D.G. Gibson, V. Setola, W. Maixner, Dokholyan, N.V., and L. Diatchenko, “Structural basis for MOR1 binding and activation”, Structure, 19:1683-1690 (2011) [download]

49. Kota, P.*, F. Ding*, Ramachandran, S.*, and Dokholyan, N.V. “Gaia: automated structure quality assessment of protein models”, Bioinformatics, 27:2209-2215 (2011) [download][service]

48. Proctor, E. A., F. Ding, and Dokholyan, N. V. “Structural and thermodynamic effects of post-translational modifications in mutant and wild type Cu, Zn superoxide dismutase”, Journal of Molecular Biology, 408:555-567 (2011). [download]

47. Ramachandran, S., Kota, P., F. Ding and Dokholyan, N. V. “Automated Minimization of Steric Clashes in Protein Structures”, Proteins: Structure, Function and Bioinformatics, 79:261-270 (2011)[download][service]

46. F. Ding, Yin, S., and Dokholyan, N. V. “Rapid flexible docking using a stochastic rotamer library of ligands”, Journal of Chemical Information and Modeling, 50:1623-32 (2010) [download]

45. A. Karginov, F. Ding, P. Kota, Dokholyan, N.V. and K. Hahn, “Engineered allosteric regulation of kinases in living cells”, Nature Biotechnology, 28:743-748, (2010) [download]

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

43. E.A. Proctor, F. Ding, and Dokholyan, N.V., “Discrete Molecular Dynamics”, Wiley Interdisciplinary Reviews: Computational Molecular Science, 1:80-92 (2010)[download]

42. V. V. Lakhani, F. Ding and N. V. Dokholyan, “Poly-glutamine induced misfolding of huntingtin exon1 is modulated by the flanking sequences” Public Library of Science Computational Biology:e1000772 (2010)[download]

41. C. Hajdin, F. Ding, N. V. Dokholyan, and K. M. Weeks, “How good is that RNA tertiary structure prediction?” RNA, 16:1340-1349 (2010) [download] [service]

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

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

38. Yin, S., F. Ding and Dokholyan, N. V. “Modeling mutations in proteins using Medusa and discrete molecular dynamics” in “Protein Structure Prediction: Method and Algorithms”, Editors: Rangwala, H. and Karypis, G. Wiley & Sons, (2009)

37. S. Yin, F. Ding, and N. V. Dokholyan, “Computational evaluation of protein stability change upon mutations using Eris.” in “In Vitro Mutagenesis Protocols” Editor: J. Braman. Humana Press (2009)

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

35. F. Ding and N. V. Dokholyan, “Dynamical roles of metal ions and the disulfide bond in Cu, Zn superoxide dismutase folding and aggregation” Proceedings of the National Academy of Sciences USA, 105:19696-19701 (2008) [download]

34. S. Sharma, F. Ding, and N. V. Dokholyan, “iFoldRNA: Three-dimensional RNA structure prediction and folding” Bioinformatics, 24:1951-1952 (2008) [download] [service]

33. D. G. Teotico, M. Frazier, F. Ding, N. V. Dokholyan, B. Temple, and M. R. Redinbo, “Active nuclear receptors exhibit highly correlated AF-2 domain motions” Public Library of Science Computational Biology, 4: e1000111 (2008) [download]

32. F. Ding, D. Tsao, H. Nie, and N. V. Dokholyan, “Ab initio folding of proteins using all-atom discrete molecular dynamics” Structure, 16: 1010-1018 (2008) [download]

31. F. Ding, S. Sharma, P. Chalasani, V. V. Demidov, N. E. Broude, and N. V. Dokholyan, “Large scale simulations of 3D RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms” RNA, 14: (2008) [download]

30. S. Sharma, F. Ding, and N. V. Dokholyan, “Probing protein aggregation using simplified models and discrete molecular dynamics” Frontiers in Bioscience, 13: 4795-4808 (2008) [download]

29. S. Yin, F. Ding, and N. V. Dokholyan, “Modeling backbone flexibility improves protein stability estimation”, Structure, 15: 1567-1576 (2007) [download]

28. A. R. Lam, J. M. Borreguero, F. Ding, N. V. Dokholyan, S. V. Buldyrev, E. I. Shakhnovich, H. E. Stanley, “Parallel folding pathways in the Src SH3 domain” Journal of Molecular Biology, 373: 1348-1360 (2007) [download]

27. S. Barton, R. Jacak, S. D. Khare, F. Ding*, and N. V. Dokholyan*, “The length dependence of the polyQ-mediated protein aggregation” Journal of Biological Chemistry, 282: 25487-25492 (2007) [download]

26. Y. Chen, F. Ding, H. Nie, A. W. Serohijos, S. Sharma, K. C. Wilcox, S. Yin, and N. V. Dokholyan, “Protein folding: then and now” Archives of Biochemistry and Biophysics, 469: 4-19 (2008) [download]

25. S. Yin, F. Ding, and N. V. Dokholyan, “Eris: An automated estimator of protein stability” Nature Methods, 4: 466-467 (2007) [download][service]

24. Y. Chen, F. Ding, and N. V. Dokholyan, “Fidelity of protein structure reconstruction from inter-residue proximity constraints” Journal of Physical Chemistry B, 111: 7432-7438 (2007) [download]

23. S. Sharma, F. Ding, and N. V. Dokholyan, “Multi-scale modeling of nucleosome dynamics” Biophysical Journal, 92 1457-1470 (2007) [download]

22. A. W. Serohijos, Y. Chen, F. Ding, T. C. Elston, and N. V. Dokholyan, “A new structural model reveals energy transduction in dynein”, Proceedings of the National Academy of Sciences USA, 103: 18540-18545 (2006)[download]

21. S. Sharma, F. Ding, H. Nie, D. Watson, A. Unnithan, J. Lopp, D. Pozefsky, and N. V. Dokholyan, “iFold: A platform for interactive folding simulations of proteins” Bioinformatics, 22: 2693-2694 (2006) [download][service]

20. F. Ding and N. V. Dokholyan, “Emergence of protein fold families through rational design” Public Library of Science Computational Biology, 2: e85 (2006) [download]

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, “Fast complementation of split fluorescent protein triggered by DNA hybridization”, Proceedings of the National Academy of Sciences USA, 103: 2052-2056 (2006). [download]

18. F. Ding, J. J. LaRocque, and N. V. Dokholyan, “Direct observation of protein folding, aggregation and a prion-like conformational transition”, Journal of Biological Chemistry, 280: 40235-40240 (2005) [download]

17. F. Ding, K. C. Prutzman, S. L. Campbell, and N. V. Dokholyan, “Topological determinants of protein domain swapping”, Structure, 14: 5-14 (2005). [download][service]

16. S. D. Khare, F. Ding, K. N. Gwanmesia, and N. V. Dokholyan, “Molecular origin of polyglutamine-mediated protein aggregation in neurodegenerative diseases”, PLoS Computational Biology, 1, e30 (2005). [download]

15. F. Ding, W. Guo, N. V. Dokholyan, E. I. Shakhnovich, and J.-E. Shea, “Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations”, J. Mol. Biol., 350: 1035-1050 (2005). [download]

14. F. Ding and N. V. Dokholyan, “Simple but predictive protein models”, Trends in Biotechnology, 23: 450-455 (2005). [download]

13. F. Ding, R. K. Jha, and N. V. Dokholyan, “Scaling behavior and structure of denatured proteins”, Structure, 13: 1047-1054 (2005). [download]

12. F. Ding, S. V. Buldyrev, and N. V. Dokholyan, “Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model”, Biophys. J., 88: 147-155 (2005). [download]

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, “New insights into FAK signaling and localization based on detection of a FAT domain folding intermediate” Structure, 12: 2161-2171 (2004). [download]

10. 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). [download]

9. J. M. Borreguero, F. Ding, S. V. Buldyrev, H. E. Stanley, and N. V. Dokholyan, “Multiple folding pathways of the SH3 domain.” Biophys. J. 87: 521-533 (2004). [download]

8. S. Peng, F. Ding, B. Urbanc, S. V. Buldyrev, L. Cruz , H. E. Stanley, and N. V. Dokholyan, “Discrete molecular dynamics simulations of peptide aggregation” Phys. Rev. E 69: 041908 (2004) [download]

7. 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 [download]

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]

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]

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]

3. Dokholyan N.V., Li L., F. Ding, et al. Topological determinants of protein folding P NATL ACAD SCI USA, 99 (13): 8637-8641 JUN 25 2002 [download]

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]

1. Lei XY, Li H, F. Ding, W Zhang, and NB Ming, Novel application of a perturbed photonic crystal: High-quality filter. APPL PHYS LETT 71 (20): 2889-2891 NOV 17 1997 [download]