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BioMed Research International
Volume 2013 (2013), Article ID 583045, 10 pages
An Alternative Approach to Protein Folding
Department of Materials Science and Engineering, Stony Brook University, Stony Brook, NY 11794-2275, USA
Received 5 April 2013; Revised 20 June 2013; Accepted 31 July 2013
Academic Editor: Rita Casadio
Copyright © 2013 Yeona Kang and Charles M. Fortmann. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- K. A. Dill, S. B. Ozkan, T. R. Weikl, J. D. Chodera, and V. A. Voelz, “The protein folding problem: when will it be solved?” Current Opinion in Structural Biology, vol. 17, no. 3, pp. 342–346, 2007.
- A. C. Clark, “Protein folding: are we there yet?” Archives of Biochemistry and Biophysics, vol. 469, no. 1, pp. 1–3, 2008.
- C. Hardin, T. V. Pogorelov, and Z. Luthey-Schulten, “Ab initio protein structure prediction,” Current Opinion in Structural Biology, vol. 12, no. 2, pp. 176–181, 2002.
- C. R. Barrett, W. D. Nix, Tetelman, and S. Alan, , Principles of Engineering Materials, Prentice Hall, New York, NY, USA, 1973.
- J. W. Moore and R. G. Pearson, Kinetics and Mechanisms, John Wiley & Sons, New York, NY, USA, 3rd edition, 1981.
- Y. Kang, E. Jaen, and C. M. Fortmann, “Einstein relations for energy coupled particle systems,” Applied Physics Letters, vol. 88, no. 11, Article ID 112110, 2006.
- Y. Kang and C. M. Fortmann, “A structural basis for the Hodgkin and Huxley relation,” Applied Physics Letters, vol. 91, no. 22, Article ID 223903, 2007.
- D. Bashford and D. A. Case, “Generalized born models of macromolecular solvation effects,” Annual Review of Physical Chemistry, vol. 51, pp. 129–152, 2000.
- J. D. Jackson, Classical Electrodynamics, Wiley & Sons, New York, NY, USA, 3rd edition, 1999.
- M. E. Glicksman, Di Usion in Solids, John Wiley & Sons, New York, NY, USA, 2000.
- Z. Peng and L. C. Wu, “Autonomous protein folding units,” Advanced in Protein Chemistry, vol. 53, pp. 1–30, 2000.
- P. Y. Chou and G. D. Fasman, “Prediction of protein conformation,” Biochemistry, vol. 13, no. 2, pp. 222–245, 1974.
- V. I. Lim, “Structural principles of the globular. Establishing homologies in protein sequences,” Journal of Molecular Biology, vol. 88, pp. 857–873, 1984.
- J. Garnier, D. J. Osguthorpe, and B. Robson, “Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins,” Journal of Molecular Biology, vol. 120, no. 1, pp. 97–120, 1978.
- G. Deleage and B. Roux, “An algorithm for protein secondary structure prediction based on class prediction,” Protein Engineering, vol. 1, no. 4, pp. 289–294, 1987.
- S. R. Presnell, B. I. Cohen, and F. E. Cohen, “A segment-based approach to protein secondary structure prediction,” Biochemistry, vol. 31, no. 4, pp. 983–993, 1992.
- H. H. L. Howard Holley l. and M. Karplus, “Protein secondary structure prediction with a neural network,” Proceedings of the National Academy of Sciences of the United States of America, vol. 86, no. 1, pp. 152–156, 1989.
- R. A. Copeland, Methods for Protein Analysis, A practical Guide to laboratory protocols, Chapman & Hall, New York, NY, USA, 1994.
- MOE, Chemical Computing Group: 1010 Sherbrooke St. W, Suite 910, Montreal, Quebec, Canada, G3A 2R7, http://www.chemcomp.com/.
- M. Guo, P. M. Gorman, M. Rico, A. Chakrabartty, and D. V. Laurents, “Charge substitution shows that repulsive electrostatic interactions impede the oligomerization of Alzheimer amyloid peptides,” FEBS Letters, vol. 579, no. 17, pp. 3574–3578, 2005.
- B. Rost and C. Sander, “Prediction of protein secondary structure at better than 70% accuracy,” Journal of Molecular Biology, vol. 232, no. 2, pp. 584–599, 1993.
- C.-Y. Lin, C.-K. Hu, and U. H. E. Hansmann, “Parallel tempering simulations of HP-36,” Proteins, vol. 52, no. 3, pp. 436–445, 2003.
- B. S. Kinnear, M. F. Jarrold, and U. H. E. Hansmann, “All-atom generalized-ensemble simulations of small proteins,” Journal of Molecular Graphics and Modelling, vol. 22, no. 5, pp. 397–403, 2004.
- W. Kwak and U. H. E. Hansmann, “Efficient sampling of protein structures by model hopping,” Physical Review Letters, vol. 95, no. 13, Article ID 138102, 4 pages, 2005.
- D. S. Marks, L. J. Colwell, R. Sheridan et al., “Protein 3D structure computed from evolutionary sequence variation,” PLoS ONE, vol. 6, no. 12, Article ID e28766, 2011.
- H. Remaut, C. Tang, N. S. Henderson et al., “Fiber formation across the bacterial outer membrane by the chaperone/usher pathway,” Cell, vol. 133, no. 4, pp. 640–652, 2008.