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The Journal of Membrane Biology

, Volume 248, Issue 6, pp 1033–1041 | Cite as

iCataly-PseAAC: Identification of Enzymes Catalytic Sites Using Sequence Evolution Information with Grey Model GM (2,1)

  • Xuan Xiao
  • Meng-Juan Hui
  • Zi Liu
  • Wang-Ren Qiu
Article

Abstract

Enzymes play pivotal roles in most of the biological reaction. The catalytic residues of an enzyme are defined as the amino acids which are directly involved in chemical catalysis; the knowledge of these residues is important for understanding enzyme function. Given an enzyme, which residues are the catalytic sites, and which residues are not? This is the first important problem for in-depth understanding the catalytic mechanism and drug development. With the explosive of protein sequences generated during the post-genomic era, it is highly desirable for both basic research and drug design to develop fast and reliable method for identifying the catalytic sites of enzymes according to their sequences. To address this problem, we proposed a new predictor, called iCataly-PseAAC. In the prediction system, the peptide sample was formulated with sequence evolution information via grey system model GM(2,1). It was observed by the rigorous jackknife test and independent dataset test that iCataly-PseAAC was superior to exist predictions though its only use sequence information. As a user-friendly web server, iCataly-PseAAC is freely accessible at http://www.jci-bioinfo.cn/iCataly-PseAAC. A step-by-step guide has been provided on how to use the web server to get the desired results for the convenience of most experimental scientists.

Keywords

Catalytic active sites Pseudo amino acid composition Grey system model Web server iCataly-PseAAC 

Notes

Acknowledgments

This work was partially supported by the National Nature Science Foundation of China (Nos. 31260273, 61261027), Natural Science Foundation of Jiangxi Province, China (Nos. 20114BAB211013, 20122BAB211033, 20122BAB201044, 20122BAB201020), the Department of Education of JiangXi Province (GJJ12490), the LuoDi plan of the Department of Education of JiangXi Province(KJLD12083), and the JiangXi Provincial Foundation for Leaders of Disciplines in Science (20113BCB22008) and the Graduated innovation found of Jingdezhen ceramic institute (JYC1310, JYC201427).

Supplementary material

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Xuan Xiao
    • 1
    • 2
    • 3
  • Meng-Juan Hui
    • 1
  • Zi Liu
    • 1
  • Wang-Ren Qiu
    • 1
  1. 1.Computer DepartmentJing-De-Zhen Ceramic InstituteJing-De-ZhenChina
  2. 2.Information SchoolZheJiang Textile & Fashion CollegeNingBoChina
  3. 3.Gordon Life Science InstituteBelmontUSA

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