Publications [#234900] of Weitao Yang

Journal Articles
  1. Xie, L; Liu, H; Yang, W, Adapting the nudged elastic band method for determining minimum-energy paths of chemical reactions in enzymes, The Journal of Chemical Physics, vol. 120 no. 17 (2004), pp. 8039-8052 [doi] .

    An efficient, robust and general approach, based on nudged elastic band reaction path optimization method, for the optimization of reaction paths for enzymatic systems was presented. The soft spectator degree of freedom were excluded from path definitions using only inter-atomic distances corresponding to forming/breaking bonds in a reaction. The applicability of the approach was demonstrated using the acylation reaction of type A β-lactamase as an example. Analysis shows that a continuous minimum energy path was obtained without any assumption on reaction coordinates.