@article {101016,
	title = {Nucleation and the Transition State of the SH3 Domain},
	journal = {Journal of Molecular Biology},
	volume = {349},
	year = {2005},
	month = {2005},
	pages = {424 - 434},
	abstract = {We present a verified computational model of the SH3 domain transition state (TS) ensemble. This model was built for three separate SH3 domains using experimental ϕ-values as structural constraints in all-atom protein folding simulations. While averaging over all conformations incorrectly considers non-TS conformations as transition states, quantifying structures as pre-TS, TS, and post-TS by measurement of their transmission coefficient ("probability to fold{\textquotedblright}, or pfold) allows for rigorous conclusions regarding the structure of the folding nucleus and a full mechanistic analysis of the folding process. Through analysis of the TS, we observe a highly polarized nucleus in which many residues are solvent-exposed. Mechanistic analysis suggests the hydrophobic core forms largely after an early nucleation step. SH3 presents an ideal system for studying the nucleation-condensation mechanism and highlights the synergistic relationship between experiment and simulation in the study of protein folding.},
	url = {http://dx.doi.org/10.1016/j.jmb.2005.03.050},
	author = {Hubner, Isaac A. and Edmonds, Katherine A. and Eugene I. Shakhnovich}
}
