About the Knowledgebase

[INTRODUCTION] [HOW TO SEARCH DATABASE] [CONTACT US] [UPDATES]



Introduction

The defensins knowledgebase is a manually curated database and information source devoted to the defensin family of antimicrobial peptides. The current version of the database holds a comprehensive collection of 363 defensin records each containing sequence, structure and activity information. A web-based interface provides access to the information and allows for text-based searching on the data fields.

With the rapidly increasing interest in defensins, we hope that the knowledgebase will prove to be a valuable resource in the field of antimicrobial peptide research.




How to search this database

Case Study 1: Retrieve all human beta-defensins records

STEP 1

Go to Defensins Knowledgebase home page at http://defensins.bii.a-star.edu.sg/

STEP 2

Click on Database search from the left hand-side menu bar

STEP 3

Restrict search by organism and family


Choose Homo sapiens from organism pull down list


Select Vertebrate Beta to restrict search to the beta family of defensins

STEP 4

SEARCH

RESULTS




Sample record for human defensin 3
Screen shot only displays the expression sites, structure and cytotoxicity information.




Contact Us


Email:




Acknowledgements


This work is supported by the Singapore Consortium for Antimicrobial Peptides (SCAMP) and the Biomedical Research Council A*STAR Singapore.

Bioinformatics Institute (BII), Singapore

Biomolecular Modeling and Design Division
Dr. Chandra Verma (Senior Research Scientist & Head of Division)
Ms. Low Soo Mei

Web Services Department
Mr. Hanafi Harron (In-Charge)

Alumni
Ms. Anita Suresh
Ms. Shalin Seebah
Mr. Zhuo Shaowei (Web Services)
Ms. Lim Zi Yun (Web Services)




ADVISORS

Singapore Eye Research Institute, Singapore
Prof. Roger Beuerman (Deputy Director, Scientific Director)




Updates


September 20 2007

The Singapore Consortium for Antimicrobial Peptides has published a short review on the therapeutic potential of defensins in Biotechnology Journal.

January 2007

The Defensins Knowledgebase has been published in Nucleic Acids Research.

August 01 2006

Basic Local Alignment Search Tool

BLAST search has been incorporated to allow users to query any sequence against the defensin sequences stored in the database. Both blastp and blastx versions are included, to support protein and nucleotide sequence queries, respectively.

Multiple Sequence Alignment

Multiple Sequence Alignment of user-selected defensin sequences from the database can be carried out using the in-built ClustalW tool. Users can select or limit sequences by family or organism. The resulting alignment can be displayed graphically using the embedded JalView applet.

Structure Viewing Tool

The molecular structures stored in the database can be viewed using either JMol or the AstexViewer™ structure viewing tools implemented in the database.

April 30 2006 - May 4 2006

Defensins Knowledgebase brochures were distributed at the ARVO-Association for Research in Vision and Ophthalmology annual meeting which was held in Fort. Lauderdale, Florida, USA and had about 8000 presentations.

A copy of the brochure is available here.