Method

CPSARST: an efficient circular permutation search tool applied to the detection of novel protein structural relationships

Wei-Cheng Lo and Ping-Chiang Lyu

Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan

author email corresponding author email

Genome Biology 2008, 9:R11doi:10.1186/gb-2008-9-1-r11

Published:	18 January 2008

Subject areas: Biochemistry and structural biology, Bioinformatics

Abstract

Circular permutation of a protein can be visualized as if the original amino- and carboxyl termini were linked and new ones created elsewhere. It has been well-documented that circular permutants usually retain native structures and biological functions. Here we report CPSARST (Circular Permutation Search Aided by Ramachandran Sequential Transformation) to be an efficient database search tool. In this post-genomics era, when the amount of protein structural data is increasing exponentially, it provides a new way to rapidly detect novel relationships among proteins.