title: Toward Identification of the reaction coordinate directly from the transition state ensemble using the kernel PCA method.
abstract: 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.
authors.affiliation: Department of Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA.
authors.forename: Dimitri
authors.initials: D
authors.lastname: Antoniou
authors.forename: Steven D
authors.initials: SD
authors.lastname: Schwartz
mesh_terms: D006801:Humans; D007770:L-Lactate Dehydrogenase / Q000737:chemistry / Q000378:metabolism; D008956:Models, Chemical; D008958:Models, Molecular; D025341:Principal Component Analysis; D011487:Protein Conformation
chemical_list: D007770:L-Lactate Dehydrogenase