Skip Navigation



Bioinformatics Advance Access published online on February 22, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti333
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
21/10/2525    most recent
bti333v1
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 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 Plewczynski, D.
Right arrow Articles by Rychlewski, L.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Plewczynski, D.
Right arrow Articles by Rychlewski, L.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received November 24, 2004
Revised January 12, 2005
Accepted February 16, 2005

Applications note

AutoMotif Server: prediction of single residue post-translational modifications in proteins

Dariusz Plewczynski 1*, Adrian Tkacz 2, Lucjan Stanislaw Wyrwicz 3, and Leszek Rychlewski 2

1 BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland; Interdisciplinary Centre for Mathematical and Computational Modeling, University of Warsaw, Warsaw, Poland
2 BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland
3 Bioinformatics Unit, Department of Physics, Adam Mickiewicz University, Poznan, Poland

* To whom correspondence should be addressed.
Dariusz Plewczynski, E-mail: darman{at}bioinfo.pl


  Abstract

The AutoMotif Server allows for identification of post-translational modification (PTM) sites in proteins based only on local sequence information. The local sequence preferences of short segments around PTM residues are described here as linear functional motifs (LFM). Sequence models for all types of PTM are trained by support vector machine on short sequence fragments of proteins in the current release of Swiss-Prot database (phosphorylation by various protein kinases, sulfation, acetylation, methylation, amidation etc.). The accuracy of the identification is estimated using the standard leave-one-out procedure. The sensitivities for all types of short LFM are in the range of 70%.

Availability: The AutoMotif Server is available free for academic use at http://automotif.bioinfo.pl/.


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 Sci.Home page
F. R. Salsbury Jr, S. T. Knutson, L. B. Poole, and J. S. Fetrow
Functional site profiling and electrostatic analysis of cysteines modifiable to cysteine sulfenic acid
Protein Sci., February 1, 2008; 17(2): 299 - 312.
[Abstract] [Full Text] [PDF]

Home page
 Protein Eng Des SelHome page
Y.-R. Tang, Y.-Z. Chen, C. A. Canchaya, and Z. Zhang
GANNPhos: a new phosphorylation site predictor based on a genetic algorithm integrated neural network
Protein Eng. Des. Sel., August 1, 2007; 20(8): 405 - 412.
[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.