Skip Navigation


Bioinformatics Advance Access originally published online on March 6, 2007
Bioinformatics 2007 23(9):1148-1155; doi:10.1093/bioinformatics/btm068
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow Supplementary data
Right arrow All Versions of this Article:
23/9/1148    most recent
btm068v1
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 arrow Search for citing articles in:
ISI Web of Science (19)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Fjell, C. D.
Right arrow Articles by Cherkasov, A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Fjell, C. D.
Right arrow Articles by Cherkasov, A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

AMPer: a database and an automated discovery tool for antimicrobial peptides

Christopher D. Fjell 1,*, Robert E.W. Hancock 2 and Artem Cherkasov 1

1Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, University of British Columbia, 2733 Heather street, Vancouver, BC, Canada, V5Z 3J5 and 2Centre for Microbial Diseases and Immunity Research, University of British Columbia, #2259 Lower Mall Research Station, Vancouver, British Columbia, V6T 1Z3, Canada

*To whom correspondence should be addressed.


  Abstract

Motivation: Increasing antibiotics resistance in human pathogens represents a pressing public health issue worldwide for which novel antibiotic therapies based on antimicrobial peptides (AMPs) may offer one possible solution. In the current study, we utilized publicly available data on AMPs to construct hidden Markov models (HMMs) that enable recognition of individual classes of antimicrobials peptides (such as defensins, cathelicidins, cecropins, etc.) with up to 99% accuracy and can be used for discovering novel AMP candidates.

Results: HMM models for both mature peptides and propeptides were constructed. A total of 146 models for mature peptides and 40 for propeptides have been developed for individual AMP classes. These were created by clustering and analyzing AMP sequences available in the public sources and by consequent iterative scanning of the Swiss-Prot database for previously unknown gene-coded AMPs. As a result, an additional 229 additional AMPs have been identified from Swiss-Prot, and all but 34 could be associated with known antimicrobial activities according to the literature. The final set of 1045 mature peptides and 253 propeptides have been organized into the open-source AMPer database.

Availability: The developed HMM-based tools and AMP sequences can be accessed through the AMPer resource at http://www.cnbi2.com/cgi-bin/amp.pl

Contact: cfjell{at}interchange.ubc.ca

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Martin Bishop

Received on May 29, 2006; revised on January 23, 2007; accepted on February 22, 2007

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
 Nucleic Acids ResHome page
S. Thomas, S. Karnik, R. S. Barai, V. K. Jayaraman, and S. Idicula-Thomas
CAMP: a useful resource for research on antimicrobial peptides
Nucleic Acids Res., January 1, 2010; 38(suppl_1): D774 - D780.
[Abstract] [Full Text] [PDF]

Home page
 Antimicrob. Agents Chemother.Home page
Z. Zhao, Y. Ma, C. Dai, R. Zhao, S. Li, Y. Wu, Z. Cao, and W. Li
Imcroporin, a New Cationic Antimicrobial Peptide from the Venom of the Scorpion Isometrus maculates
Antimicrob. Agents Chemother., August 1, 2009; 53(8): 3472 - 3477.
[Abstract] [Full Text] [PDF]

Home page
 FASEB J.Home page
B. Gao, P. Sherman, L. Luo, J. Bowie, and S. Zhu
Structural and functional characterization of two genetically related meucin peptides highlights evolutionary divergence and convergence in antimicrobial peptides
FASEB J, April 1, 2009; 23(4): 1230 - 1245.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
G. Wang, X. Li, and Z. Wang
APD2: the updated antimicrobial peptide database and its application in peptide design
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D933 - D937.
[Abstract] [Full Text] [PDF]

Home page
 Antimicrob. Agents Chemother.Home page
C. Dai, Y. Ma, Z. Zhao, R. Zhao, Q. Wang, Y. Wu, Z. Cao, and W. Li
Mucroporin, the First Cationic Host Defense Peptide from the Venom of Lychas mucronatus
Antimicrob. Agents Chemother., November 1, 2008; 52(11): 3967 - 3972.
[Abstract] [Full Text] [PDF]

Home page
 Antimicrob. Agents Chemother.Home page
C. Gelhaus, T. Jacobs, J. Andra, and M. Leippe
The Antimicrobial Peptide NK-2, the Core Region of Mammalian NK-Lysin, Kills Intraerythrocytic Plasmodium falciparum
Antimicrob. Agents Chemother., May 1, 2008; 52(5): 1713 - 1720.
[Abstract] [Full Text] [PDF]

Home page
 Antimicrob. Agents Chemother.Home page
W. S. Jang, S.-C. Lee, Y. S. Lee, Y. P. Shin, K. H. Shin, B. H. Sung, B. S. Kim, S. H. Lee, and I. H. Lee
Antimicrobial Effect of Halocidin-Derived Peptide in a Mouse Model of Listeria Infection
Antimicrob. Agents Chemother., November 1, 2007; 51(11): 4148 - 4156.
[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.