Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (PDF) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (5)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Shionyu-Mitsuyama, C.
Right arrow Articles by Yamane, T.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Shionyu-Mitsuyama, C.
Right arrow Articles by Yamane, T.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Protein Engineering vol. 16 no. 7 pp. 467-478, 2003
© 2003 Oxford University Press

An empirical approach for structure-based prediction of carbohydrate-binding sites on proteins

Clara Shionyu-Mitsuyama1, Tsuyoshi Shirai2,3, Hirokazu Ishida4 and Takashi Yamane1

1Department of Biotechnology and Biomaterial Chemistry, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, 2Department of Computational Biology, Biomolecular Engineering Research Institute, 6-2-3, Furuedai, Suita, Osaka 565-0874 and 4Advanced IT Development Department, CTI Co., Ltd, Meieki-Minami 1-27-2, Nakamura-ku, Nagoya 450-0003, Japan

3 To whom correspondence should be addressed. e-mail: shirai{at}beri.or.jp

A computer program system was developed to predict carbohydrate-binding sites on three-dimensional (3D) protein structures. The programs search for binding sites by referring to the empirical rules derived from the known 3D structures of carbohydrate–protein complexes. A total of 80 non-redundant carbohydrate–protein complex structures were selected from the Protein Data Bank for the empirical rule construction. The performance of the prediction system was tested on 50 known complex structures to determine whether the system could detect the known binding sites. The known monosaccharide-binding sites were detected among the best three predictions in 59% of the cases, which covered 69% of the polysaccharide-binding sites in the target proteins, when the performance was evaluated by the overlap between residue patches of predicted and known binding sites.

Received April 24, 2003; revised June 2, 2003; accepted June 10, 2003.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Protein Eng Des SelHome page
T. Nakahara, O. Hindsgaul, M. M. Palcic, and S.-I. Nishimura
Computational design and experimental evaluation of glycosyltransferase mutants: engineering of a blood type B galactosyltransferase with enhanced glucosyltransferase activity
Protein Eng. Des. Sel., December 1, 2006; 19(12): 571 - 578.
[Abstract] [Full Text] [PDF]

Home page
 Protein Eng Des SelHome page
M. Saito, M. Go, and T. Shirai
An empirical approach for detecting nucleotide-binding sites on proteins
Protein Eng. Des. Sel., February 1, 2006; 19(2): 67 - 75.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.