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Article

Temperature-Dependent Probabilistic Roadmap Algorithm for Calculating Variationally Optimized Conformational Transition Pathways

Haijun Yang,^† Hao Wu,^† Dawei Li,^† Li Han,*^‡ and Shuanghong Huo*^†

Gustaf H. Carlson School of Chemistry and Biochemistry and Department of Mathematics and Computer Science, Clark University, 950 Main Street, Worcester, Massachusetts 01610

J. Chem. Theory Comput., 2007, 3 (1), pp 17–25

DOI: 10.1021/ct0502054

Publication Date (Web): November 15, 2006

†

Gustaf H. Carlson School of Chemistry and Biochemistry.

Corresponding author fax: (508) 793-8861; e-mail: shuo@ clarku.edu (S.H.) and fax: (508) 421-3715; e-mail: lhan@ clarku.edu (L.H.).

‡

Department of Mathematics and Computer Science.

Abstract

In this paper we present a method to calculate a temperature-dependent optimized conformational transition pathways. This method is based on the maximization of the flux derived from the Smoluchowski equation and is implemented with a probabilistic roadmap algorithm. We have tested the algorithm on four systemsthe Müller potential, the three-hole potential, alanine dipeptide, and the folding of β-hairpin. Comparison is made with existing algorithms designed for the calculation of protein conformational transition and folding pathways. The applications demonstrate the ability of the algorithm to isolate a temperature-dependent optimal reaction path with improved sampling and efficiency.