PolySacDb

A Database of Polysachharide 3D structures

 
By A. Sarkar & S. Pérez
   
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User Guide

PolySac3DB© is a curated and annotated database and information portal for the 3D structures (atomic coordinates) of polysaccharide structures. The structures available on this database have been extracted from publications in peer-reviewed journals (References provided). This is an effort to organize experimental as well as theoretical (molecular modelling) data on the 3D structure of polysaccharides in one repository. It is freely available over the internet for scientific and educational purposes.

HOME page :

This provides the user with an introduction to polysaccharides and sneek-peek in to the data and what the user should expect to find in the database.

 

SEARCH page :

The polysaccharide data oragnized in the database can be browsed starting from the SEARCH page. The data can be accessed in 2 ways:

Search by NAME searches the database by just knowing the name of the polysaccharide of interest (available through a drop-down button that enlists all the polysaccharides present in PolySac3DB© ).

Search by FAMILY groups all the entries in the database into 18 groups / families to clearly categorize the overall properties to be expected from those polysaccharides, where they are found in nature etc.

 

As PolySac3DB© is intended to be an information repository as well as a source of polysaccharide education, we have kept in mind aims of different users. The user can browse the data using 2 different modes provided which suits their specific needs.

DISCOVER pages are well-annotated information that presents to the user an introduction of the respective polysaccharide family, its constituent members, their major function(s), where they are found, the advances made in the structure determination of the member(s) of the family interspersed with appropriate illustrations and references.

 

EXPERT pages, as the name suggests, is directed towards experts, who already know about their polysaccharide and the background information and are looking to gather structural data available for it from one repository. This page provides information like diffraction diagrams (if the structure has been determined by diffraction experiments), the 3D structures (repeat unit and expanded / helical form) for viewing and download (in formats compatible with protein structures to ease simulation studies on protein-carbohydrate interactions). Also as these structures are made available in the general formats compatible with proteins, no special visualisation tool is required to view the structures once downloaded. These pages also provide information and links to the abstract of the publications from which the structures have been taken and other relevant structure-associated information.

 

BUILD (with POLYS) page :

This is a future plan to incorporate a web-version of POLYS which is a molecular builder for polysaccharides and oligosaccharides. This shall empower the user the build his/her own polysaccharide helices by simply specifying the COMPOSITION (constituent monosaccharides) and their TOPOLOGY (the specific linkages that link these constituent monosaccharide units).

 

METHODS page :

These are informative pages on how Molecular Modelling and experimental techniques like X-ray, Electron & Neutron Diffraction are specifically employed to determine the structure of polysaccharides.

 

REFERENCE page :

The REFERENCE page has a list of all the publications from which atomic coordinates of polysaccharide structures have been extracted to be put in to this database.

 

 

ABOUT page :

This is some information about the research interests of our group (Glycobiologie Moléculaire) at CERMAV .

 

 

CONTACT US page :

We welcome queries / suggestions about the database and shall be glad to incorporate more and more polysaccharide 3D structures that have been published. Please contact us at the addresses and numbers provided.

 

 

 

     
   
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