Temperature-dependent probabilistic roadmap algorithm for calculating variationally optimized conformational transition pathways

Authors

Haijun Yang, Clark University
Hao Wu, Clark University
Dawei Li, Clark University
Li Han, Clark UniversityFollow
Shuanghong Huo, Clark University

Document Type

Article

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 systems-the Müller potential, the three-hole potential, alanine dipeptide, and the folding of ß-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. © 2007 American Chemical Society.

Publication Title

Journal of Chemical Theory and Computation

Publication Date

2007

Volume

3

Issue

1

First Page

17

Last Page

25

ISSN

1549-9618

DOI

10.1021/ct0502054

Repository Citation

Yang, Haijun; Wu, Hao; Li, Dawei; Han, Li; and Huo, Shuanghong, "Temperature-dependent probabilistic roadmap algorithm for calculating variationally optimized conformational transition pathways" (2007). Computer Science. 199.
https://commons.clarku.edu/faculty_computer_sciences/199

APA Citation

Yang, H., Wu, H., Li, D., Han, L., & Huo, S. (2007). Temperature-dependent probabilistic roadmap algorithm for calculating variationally optimized conformational transition pathways. Journal of chemical theory and computation, 3(1), 17-25.