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Protein folding

Topics:

a) Protein folding thermodynamics and kinetics

b) Protein folding transition states

c) Protein folding pathways

d) Ab initio protein folding

 

References:

15. 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, in press [download] (2012)

14. 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]

13. 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]

12. 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]

11. 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]

10. 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]

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

8. 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]

7. 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]

6. 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]

5. 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]

4. 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]

3. 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]

2. 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]

1. 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]