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 News               (Last update 2014.10.5)
ATDB 2.5 updated (2010.10.5)
We have updated the toxin sequence and classifed them into Toxin ontology. The interaction of them with ion channel also updated.
ATDB 2.0 updated (2009.7.30)
We have updated the search engry and download web page and repaired some bugs. Jmol plugs has been used to show 3D structure information.

ATDB version 2.0 release (2009.2.25)
ATDB 2.0 has been constructed by a toxin ligand database which included by 5097 ion channel sequences. In which, more than 1000 sequences of ion channel have been annotated manually and 10956 ion channel ontology terms have been created. More than 3000 interaction network maps have been drawn.

ATDB version 1.5 release (2008.8.13)
609 new toxin sequences and related annotations have been imported into ATDB. The toxin pdb file now can be showed in our website. And a new page named "High Light" was opened to highlight the breakthroughs of toxin research.

Publication (2007.10.15)
The paper about ATDB database has been accepted by Nucleic Acid Research and will be published on the 2008 Database issue. It now can be downloaded from here.

ATDB version 1.2 release (2007.9.13)
743 additional TO annotations have been added. TO envidenceare codes were assiged to all of TO annotations.

Web site update (2007.8.8)
The Web site was updated to be compatible with "Firefox" browser and the functions of "Text search" and "Filter" were optimized.

ATDB version 1.1 release (2007.7.10)
After integrating data from other databases, 895 new entries have been imported into the ATDB. 1420 TO terms are assigned to these entries. Now, the version of the database is 1.1.

News subject (2007.7.5)
News subject about ATDB upgrades was opened in the New&FAQ page for recording the history of ATDB.

Small molucles (2007.7.5)
Five well known small molecule toxins have been imported into the databases including Tetrodotoxin, Batrachotoxin, Saxitoxin, Ciguatoxin, Maitotoxin.

Species tree update (2007.6.28)
The species tree has been updated. 128 pictures and 48 descriptions about species have been add to datbase.

ATDB version 1.0 release (2007.6.20)
ATDB 1.0 release. It deposits 2340 peptide toxins from 389 species. Most of them are annotated manually using more than 7000 TO terms.

External links
International Society on Toxinology (IST)
Toxin annotation program (Tox-Prot)

 

Frequently Asked Questions:
1) Why integrate a ligand database in ATDB and why ion channels are the major components in ligand database?
2) How to show 3D structure in a web page?
3) What are the differences between ATDB 2.0 and ATDB 1.0?
4) How to browse interaction network of toxin or ion channel and use Interaction summary?
5) How to use Interaction view?
6) What are the differences between ATDB and other toxin databases?
7) Given a protein name, how can I find all annotations of them?
8) What is the Toxin Ontology? Why?
9) The view of Ontology looks complex, how to operate it?
10) How can I extract toxins preferred basic on function, structure as well species information?
11) How do I submit a suggestion or a new toxin to the database?
12) How can I download data from ATDB?
13) What is the expected update cycle of the database?
14) Why can't the database work properly on my browsers?
15) What is the TO evidence codes?
16) Is a license required to download and use the ATDB data?


1) Why integrate a ligand database in ATDB and why ion channels are the major components in ligand database?
ATDB 2.0 focus on toxin interaction. So to construct a ligand database is nessary. A comprehensive knowledge about toxin target is indispensable for describing a T-C interaction. Although various molecules targeted by animal toxins, ion channels, as the largest group of toxin targets, are undoubtedly the most important ones. Many toxins, especially neurotoxins, act by affecting ion channels to increase or decrease ion permeability of the excitable cell membrane with high specific and efficient ways, which leads to paralysis and eventually death.

2) How to show 3D structure in web page?
In the laste version, Users don't download pluge in to localction PC but must update Java to 6.0 or later.

3) What are the differences between ATDB 2.0 and ATDB 1.0?
ATDB 2.0 focuses on interaction between toxin and ion channel. It supports different views to express toxins characteristic property than ATDB 1.0

4) How to browse interaction network of toxin or ion channel and use Interaction summary?
a) “Interaction” is a submenu which should been found from Brow popup-menu. Click submenu "by toxin" or "by ion channel" to relative web page.
b) "by interaction" is a submenu which should been found form Toxin or Ion channel at Brow popup-menu. Click them, the web page will been opened to show relative information about toxin or ion channel interaction.
c) Open "Site map", you will find it from How popup-menu and click it. You will find the information about interaction on site map, and then click it, the interacion web pape will showing.

5) How to use Interaction view?
Interaction network view of ion channel (CT0003728) with toxins. (1) Map of interaction network between the channel (the read node in the center) and toxins (other nodes). All toxins are grouped/shaped and colored according to their taxonomic classification and activity. Users can access detailed molecular information by clicking the node. The interactions between toxins and ion channel are represented by edges which are colored according to their confidence degree (see below). (2) Statistics matrix of toxins classification based on the taxonomic and activity type (active, inhibit and unknown) information. Users can retrieve a corresponding toxin list by clicking each well of the matrix. (3, 4) Topology structure and possible interact sites of the ion channel. (5) Legend about five confidence degrees (Very Low, Low, Normal, High, Very High). (6) Channel ID and taxon information. (7) Channel basic information. (8) Target list which molecular are interaction with channel protein. (9) A select list for selecting data according to confident degree.

6) What are the differences between ATDB and other toxin databases?
The targets of ATDB are collecting all of animal toxins and constructing uniform classification/annotation systems for them. So the biggest difference of ATDB to other previous toxin databases is that it is not limited within certain taxonomic groups and uses controlled terms to descript toxin functions.

7) Given a protein name, how can I find all annotations of them?
Solution: Go to Text search page, select the type of ID from list, and input the protein ID and then click the search button. Notice: the search engine allows a batch search with protein ID list in same type separated by split char “|?

8) What is the Toxin Ontology? Why?
The Toxin Ontology is a structured, controlled vocabularies for consistent descriptions of toxin function and characters. It contains four term spaces and more than 700 distinct terms. In ATDB, all toxins have been annotated by more than 7000 TO terms in total. A detailed introduction can be found here. In ATDB 2.0, TO is a name of ontology system which include two ontology, one is Toxin Ontology and the other is Ion Channel Ontology.

9) The view of Ontology looks complex, How to operate it?

Each TO namespace has a view for browsing. (1) They include a left tree and a right table. You can focus and expand the branches of the tree by clicking leaves (terms) and detail about the terms will be show in the table. (2) If you want to get all toxins related the term, just click getSequence button and an entry list will display. (3,4,5) Filtering and selecting manually can be done via a filter through keyword matches. (6) The selected sequences can be downloaded smoothly as an Excel file and Fasta file by push the Excel download and Fasta download button respectively.

10) How can I extract toxins preferred basic on function, structure as well species information?
Thanks to the detailed classification system of TO and flexible query system, users can get toxins they are interested in accurately by browsing TO views and advanced text search. A BLAST search engine is also available for sequence query.

11) How do I submit a suggestion or a new toxin to the database?
Any suggestions are welcome and can be submitted via Submission page or email to hqyone@hotmail.com or liangsp@hunnu.edu.cn. As to new entry register, we recommend that new sequence(s) should be submitted to a general database such as GenBank and SwissProt firstly and then inform us via the similar way as suggestion submission. As to small molecules or other type toxins, please email us directly. Detailed information about the author(s), taxon and function is required. We will check it and reply within four business days.

12) How can I download data from ATDB?
All data of ATDB toxin is available to public. User can download it via Download page.

13)What is the expected update cycle of the database.
The major update cycle of ATDB is two months, small revision is timely.

14) Why the database cannot work properly on my browsers?
The application has been developed in a Windows Internet Explorer context. Some differences of html protocols applied by various browsers may result in the problem. We have noticed the issue and will fix it in the update versions. In current status, we recommend you Internet Explorer 6.0 or laters and firefox browser.

15) What is the TO evidence codes?
Every annotation must be attributed to a source, which may be a literature reference, another database or a computational analysis. There are five TO evidence codes:

ISS 
 inferred from sequence or structural similarity.
IDA  
 inferred from direct assay.[from <Pubmed>]
IEA  
 inferred from electronic annotation.
TAS  
 traceable author statement.
IC  
 inferred by curator.[from <GO:id> or <Database ID>]

16) Is a license required to download and use the ATDB data?
There license condition attached to the non-commercial use of the ATDB database. For commercial use, entries in ATDB are copyright and advance permission is required. Please contact with Prof. Song-Ping Liang ( liangsp@hunnu.edu.cn ) supervisor of ATDB.

   
       
   
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