Skip Navigation



Bioinformatics Advance Access published online on December 7, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti179
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
21/8/1415    most recent
bti179v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
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 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 arrowRequest Permissions
Google Scholar
Right arrow Articles by Zhao, E.
Right arrow Articles by Kao, C.-Y.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Zhao, E.
Right arrow Articles by Kao, C.-Y.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics © Oxford University Press 2004; all rights reserved.
Received July 18, 2004
Revised October 29, 2004
Accepted November 23, 2004

Article

Cysteine separations profiles (CSP) on protein sequences infer disulfide connectivity

East Zhao 1, Hsuan-Liang Liu 2, Chi-Hung Tsai 1, Huai-Kuang Tsai 1, Chen-hsiung Chan 1, and Cheng-Yan Kao 1*

1 Bioinformatics Laboratory, Department of Computer Science and Information Engineering, National Taiwan University, No. 1 Sec. 4 Roosevelt Rd., Taipei, Taiwan 106
2 Department of Chemical Engineering and Graduate Institute of Biotechnology, National Taipei University of Technology No. 1 Sec. 3 Chung-Hsiao E. Rd., Taipei, Taiwan 10608

* To whom correspondence should be addressed.
Cheng-Yan Kao, E-mail: cykao{at}csie.ntu.edu.tw


  Abstract

Motivation: Disulfide bonds play an important role in protein folding. A precise prediction of disulfide connectivity can strongly reduce the conformational search space and increase the accuracy in protein structure prediction. Conventional disulfide connectivity predictions use sequence information, and prediction accuracy is limited. Here, by using an alternative scheme with global information for disulfide connectivity prediction, higher performance is obtained with respect to other approaches.

Result: Cysteine separation profiles (CSPs) have been used to predict the disulfide connectivity of proteins. The separations among oxidized cysteine residues on a protein sequence have been encoded into vectors named cysteine separation profiles (CSPs). Through comparisons of their CSPs, the disulfide connectivity of a test protein is inferred from a non-redundant template set. For non-redundant proteins in SwissProt 39 (SP39) sharing less than 30% sequence identity, the prediction accuracy of a four-fold cross validation is 49%. The prediction accuracy of disulfide connectivity for proteins in SwissProt 43 (SP43) is even higher (53%). The relationship between the similarity of CSPs and the prediction accuracy is also discussed. The method proposed in this work is relatively simple and can generate higher accuracies comparing to conventional methods. It may be also combined with other algorithms for further improvements in protein structure prediction.

Availability: The program and datasets are available from the authors upon request.


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
 BioinformaticsHome page
R. Rubinstein and A. Fiser
Predicting disulfide bond connectivity in proteins by correlated mutations analysis
Bioinformatics, February 15, 2008; 24(4): 498 - 504.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J. Song, Z. Yuan, H. Tan, T. Huber, and K. Burrage
Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure
Bioinformatics, December 1, 2007; 23(23): 3147 - 3154.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. Ceroni, A. Passerini, A. Vullo, and P. Frasconi
DISULFIND: a disulfide bonding state and cysteine connectivity prediction server.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W177 - W181.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
C.-H. Tsai, B.-J. Chen, C.-h. Chan, H.-L. Liu, and C.-Y. Kao
Improving disulfide connectivity prediction with sequential distance between oxidized cysteines
Bioinformatics, December 15, 2005; 21(24): 4416 - 4419.
[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.