The Community for Technology Leaders
RSS Icon
Issue No.02 - March-April (2012 vol.14)
pp: 97-103
<p>By studying the atomistic interactions involved, computer simulation has greatly helped scientists understand fundamental aspects of protein folding. Here, we review the advantages and shortcomings of some current computer simulation methods.</p>
Protein folding, computer simulation, computational science, scientific computing
Leili Javidpour, "Computer Simulations of Protein Folding", Computing in Science & Engineering, vol.14, no. 2, pp. 97-103, March-April 2012, doi:10.1109/MCSE.2012.21
1. B. Schuler and W.A. Eaton, "Protein Folding Studied by Single-Molecule FRET," Current Opinion in Structural Biology, vol. 18, no. 1, 2008, pp. 16–26.
2. A.R. Fersht, "Structure and Mechanisms in Protein Science: A Guide to Enzyme Catalysis and Protein Folding," 9th ed., Freeman, New York, 2008.
3. C. Branden and J. Tooze, Introduction to Protein Structure, 2nd ed., Garland Publishing, New York, 1998.
4. H.M. Berman et al., "The Protein Data Bank," Nucleic Acids Research, vol. 28, no. 1, 2000, pp. 235–242.
5. J.R. Banavar et al., "Unified Perspective on Proteins: A Physics Approach," Physical Rev. E, vol. 70, no. 4, 2004; doi:10.1103/PhysRevE.70.041905.
6. C.M. Dobson, "Protein Folding and Misfolding," Nature, vol. 426, no. 6968, 2003, pp. 884–890.
7. K.A. Dill et al., "Protein Folding Problem," Ann. Rev. Biophysics, vol. 37, no. 1, 2008, pp. 289–316; doi:10.1146/annurev.biophys.37.092707.153558.
8. C.B. Anfinsen, "Principles that Govern the Folding of Protein Chains," Science, vol. 181, no. 4096, 1973, pp. 223–230.
9. S. Takada, Z. Luthey-Schulten, and P.G. Wolynes, "Folding Dynamics with Nonadditive Forces: A Simulation Study of a Designed Helical Protein and a Random Heteropolymer," J. Chemical Physics, vol. 110, no. 23, 1999; doi:10.1063/1.479101.
10. L. Mirny and E. Shakhnovich, "Protein Folding Theory: From Lattice to All-Atom Models," Ann. Rev. Biophysics and Biomolecular Structures, vol. 30, 2001, pp. 361–396.
11. J. Kubelka, J. Hofrichter, and W.A. Eaton, "The Protein Folding Speed Limit," Current Opinion in Structural Biology, vol. 14, no. 1, 2004, pp. 76–88.
12. F.U. Hartl and M. Hayer-Hartl, "Concepts of Protein Folding In Vitro and In Vivo," Nature Structural & Molecular Biology, vol. 16, 2009, pp. 574–581.
13. C. Clementi, H. Nymeyera, and J.N. Onuchic, "Topological and Energetic Factors: What Determines the Structural Details of the Transition State Ensemble and 'En-route' Intermediates for Protein Folding? An Investigation for Small Globular Proteins," J. Molecular Biology, vol. 298, no. 5, 2000, pp. 937–953.
14. L. Javidpour and M. Sahimi, "Confinement in Nanopores Can Destabilize Alpha-Helix Folding Proteins and Stabilize the Beta Structures," J. Chemical Physics, vol. 135, no. 12, 2011; doi:10.1063/1.3641482.
15. M.P. Allen and D. Tildesley, Computer Simulation of Liquids, Clarendon Press, Oxford, 1987.
16. Y. Duan and P.A. Kollman, "Pathways to a Protein Folding Intermediate Observed in a 1-Microsecond Simulation in Aqueous Solution," Science, vol. 282, no. 5389, 1998, pp. 740–744.
17. V.A. Voelz et al., "Molecular Simulation of Ab Initio Protein Folding for a Millisecond Folder NTL9 (139)," J. Am. Chemical Soc., vol. 132, no. 5, 2010, pp. 1526–1528.
18. H.D. Nguyen and C.K. Hall, "Molecular Dynamics Simulations of Spontaneous Fibril Formation by Random-Coil Peptides," Proc. Nat'l Academy of Science, Nat'l Academy of Sciences, vol. 101, no. 46, 2004, pp. 16180–16185.
19. L. Javidpour, M.R. Rahimi Tabar, and M. Sahimi, "Molecular Simulation of Protein Dynamics in Nanopores. II. Diffusion," J. Chemical Physics, vol. 130, no. 8, 2009; doi:10.1063/1.3080770.
20. L. Javidpour, M.R. Rahimi Tabar, and M. Sahimi, "Molecular Simulation of Protein Dynamics in Nanopores. I. Stability and Folding," J. Chemical Physics, vol. 128, no. 11, 2008; doi:10.1063/1.2894299.
120 ms
(Ver 2.0)

Marketing Automation Platform Marketing Automation Tool