Glycoinformatics

Glycoinformatics

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Glycoinformatics is a relatively new field of bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...

 that pertains to the study of carbohydrates. It broadly includes (but is not restricted to) database
Database
A database is an organized collection of data for one or more purposes, usually in digital form. The data are typically organized to model relevant aspects of reality , in a way that supports processes requiring this information...

, software, and algorithm
Algorithm
In mathematics and computer science, an algorithm is an effective method expressed as a finite list of well-defined instructions for calculating a function. Algorithms are used for calculation, data processing, and automated reasoning...

 development for the study of carbohydrate structures
Polysaccharide
Polysaccharides are long carbohydrate molecules, of repeated monomer units joined together by glycosidic bonds. They range in structure from linear to highly branched. Polysaccharides are often quite heterogeneous, containing slight modifications of the repeating unit. Depending on the structure,...

, glycoconjugates
Glycoconjugates
Glycoconjugates is the general classification for carbohydrates covalently linked with other chemical species.Glycoconjugates are very important compounds in biology and consist of many different categories such as glycoproteins, glycopeptides, peptidoglycans, glycolipids, and lipopolysaccharides...

, enzymatic carbohydrate synthesis
Chemical synthesis
In chemistry, chemical synthesis is purposeful execution of chemical reactions to get a product, or several products. This happens by physical and chemical manipulations usually involving one or more reactions...

 and degradation
Chemical decomposition
Chemical decomposition, analysis or breakdown is the separation of a chemical compound into elements or simpler compounds. It is sometimes defined as the exact opposite of a chemical synthesis. Chemical decomposition is often an undesired chemical reaction...

, as well as carbohydrate interactions. Conventional usage of the term does not currently include the treatment of carbohydrates from the more well-known nutritive
Nutrition
Nutrition is the provision, to cells and organisms, of the materials necessary to support life. Many common health problems can be prevented or alleviated with a healthy diet....

 aspect.

Complexity


Carbohydrates or "sugars" (this term should not be confused with simple sugars - monosaccharides and disaccharides) as they are generally called, form the third class of biopolymers, other two being proteins and nucleic acids. Unlike proteins and nucleic acids which are linear, carbohydrates are often branched and extremely complex. For instance, just four sugars can be strung together to form more than 5 million different types of carbohydrates or nine different sugars may be assembled into 15 million possible four-sugar-chains. Despite their repetitive nature, carbohydrates are often considered as the "information poor" molecules. Consequently, bioinformatics on glycome
Glycome
The glycome is the entire complement of sugars, whether free or present in more complex molecules, of an organism. An alternative definition is the entirety of carbohydrates in a cell. The glycome may in fact be one of the most complex entities in nature...

 is also very poor.

Sequence representation


Owing to the lack of a genetic blue print, carbohydrates do not have a "fixed" sequence. Instead, the sequence is largely determined by the kinetic differences in the enzyme
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...

s and variations in the biosynthetic micro-environment of the cells.

One of the main constrains in the glycoinformatics is the difficulty of representing sugars in the sequence form especially due to their branching nature.

The sequence of branching information in a carbohydrate molecule is represented in the figure.