Journal of Physical Chemistry B, Vol.115, No.10, 2465-2469, 2011
Toward Identification of the Reaction Coordinate Directly from the Transition State Ensemble Using the Kernel PCA Method
We propose a new method for analyzing an ensemble of transition states to extract components of the reaction coordinate. We use the kernel principal component analysis (kPCA), which is a generalization of the ordinary PCA that does not make a linearization approximation We applied this method to a TPS study of human LDH we had previously published [Quaytman, S.; Schwartz, S. D. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 12253] and extracted a reasonable representation for the reaction coordinate.