Abstract
Protein folding simulations have contributed significantly to our understanding of the problem, since it is difficult to study individual molecules during the folding process. We have recently performed folding simulations of Chignolin, a decapeptide (Seibert et al., J. Mol. Biol. 354 (2006) p. 173) and introduced a new algorithm for deriving kinetics information as well as thermodynamics from the trajectories (Van der Spoel & Seibert, Phys. Rev. Lett. 96 (2006), p. 238102). Here we investigate the algorithm further and show that the folding reaction for Chignolin is a two-state folding reaction, in accord with experimental data.
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van der Spoel, D., Patriksson, A., Seibert, M.M. (2007). Protein Folding Properties from Molecular Dynamics Simulations. In: Kågström, B., Elmroth, E., Dongarra, J., Waśniewski, J. (eds) Applied Parallel Computing. State of the Art in Scientific Computing. PARA 2006. Lecture Notes in Computer Science, vol 4699. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-75755-9_13
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DOI: https://doi.org/10.1007/978-3-540-75755-9_13
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