Contents :

:: Searching in HaptenDB
:: Browsing HaptenDB
:: Submiting Data in HaptenDB
:: Reporting Errors and Broken Links
:: Using SRS Version
:: Chemical File Formats

Searching in HaptenDB

Keyword Search

Enter the Query Terms in the Textbox and select the Fields under which you want to perform your search choose All fields if you want to search all fields, use and / or to further refine your search. You can also select the group ofcompounds and the host organism under which you want to perform your search. You also choose how many results you want to display on one page and then click over the 'Search HaptenDB' button to run your query. The query text be at least 3 character long.

The result for the query will be displayed as under

Clicking on Detail of a single record will show the complete detail of the concerned record

Searching using Structures

Users can also perform query in the database using their own haptens. this allows submiting of a hapten in a recognizable chemical format and specifying type of search viz. substruture / perfect / exact / superstructure search . The server will then perform a search using jcsearch command line utility of JChem.

This option takes a little time for its execution, since aligning submitted molecules and evaluting similarity matrices are highly processing intensive tasks.

Browsing in HaptenDB

HaptenDB also provides tools to fully browse all the data contained in the database. The database for this purpose is divided into three entities i.e. Hapten, associated Carrier proteins(carriers), Hapten Antibodies, a user can browse the database by hapten, carrier and antibodies by selecting the appropiate links it will display summary records for all the records contained in the database.

A browse page for an antibodies is shown as under :

Submitting data in HaptenDB

The web server allows user to submit their hapten and related antibodies on-line by filling a HTML form. Users can either submit haptens or hapten antibodies, the data submitted by the users is thoroghly normalized and validated before being added to HaptenDB web server

In order to maintain the consistency we will release HaptenDB database quaterly. All haptens obtain during two release will be available as new submissions. The success of this database is highly depend upon contributor, please enter the new haptens in HaptenDB or iinform our team so that we can include more and more haptens in database.

Reporting errors and Broken links

Users are requested to report errors in the content or presentation to the HaptenDB team, so as to correct such mistakes if any as early as possible. Users can report such errors and broken links by sending an email to grish@imtech.res.in

Using SRS Version

The SRS Version of the database is available at :
http://www.imtech.res.in/srs5bin/cgi-bin/wgetz?-fun+pagelibinfo+-info+HAPTENDB .

Chemical File Formats

Different Chemical file formats currently supported by HaptenDB web server are as under :

The HaptenDB Web Server internall uses only MOL file format and all other file formats while be converted to MOL Files for internal processing and conversions. The MOL File Format is discussed in greater details as under :

MOL File Format

A mol file consists of a header block and a connection table. The following shows a mol file for alanine corresponding to the following structure:

The format for a mol file is

• Header Block : Identifies the mol file: molecule name, user's name, program, date, and other miscellaneous information and comments
• Ctab Block : A connection table (Ctab) contains information describing the structural relationships and properties of a collection of atoms. The atoms may be wholly or partially connected by bonds. Such collections may, for example, describe molecules, molecular fragments, substructures, substituent groups, polymers, alloys, formulations, mixtures, and unconnected atoms.
• Counts line: Important specifications here relate to the number of atoms, bonds, and atom lists, the chiral flag setting, and the Ctab version.
• Atom block: Specifies the atomic symbol and any mass difference, charge, stereochemistry, and associated hydrogens for each atom.
• Bond block: Specifies the two atoms connected by the bond, the bond type, and any bond stereochemistry and topology (chain or ring properties) for each bond.
• Properties block: Provides for future expandability of Ctab features, while maintaining