2005/04/29 by Joanne M. Carr, Semen A. Trygubenko, David J. Wales · 176 citations
Biochemistry, Genetics and Molecular Biology · Computer Science · Physics and Astronomy · #Computational Drug Discovery Methods #Convergence (economics) #Domain (mathematical analysis) #Euclidean distance #Folding (DSP implementation) #Function (biology) #Maxima and minima #Metric (unit) #Path (computing) #Protein Structure and Dynamics #Saddle point #Topological and Geometric Data Analysis #cond-mat.other
paper · pdf · doi:10.1063/1.1931587
published in The Journal of Chemical Physics 122(23), 234903 (American Institute of Physics) · 29 pages, 4 figures
arxiv created 2005/04/29 · openalex publication_date 2005/06/15 · arxiv updated 2009/12/01 · openalex created_date 2016/06/24 · openalex updated_date 2026/08/05
We report a new algorithm for constructing pathways between local minima that involve a large number of intervening transition states on the potential energy surface. A significant improvement in efficiency has been achieved by changing the strategy for choosing successive pairs of local minima that serve as endpoints for the next search. We employ Dijkstra's algorithm [E. W. Dijkstra, Numer. Math. 1, 269 (1959)] to identify the "shortest" path corresponding to missing connections within an evolving database of local minima and the transition states that connect them. The metric employed to determine the shortest missing connection is a function of the minimized Euclidean distance. We present applications to the formation of buckminsterfullerene and to the folding of various biomolecules: the B1 domain of protein G, tryptophan zippers, and the villin headpiece subdomain. The corresponding pathways contain up to 163 transition states and will be used in future discrete path sampling calculations.