Glycoinformatics is a field of

bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...

that pertains to the study of

carbohydrates In organic chemistry, a carbohydrate () is a biomolecule consisting of carbon (C), hydrogen (H) and oxygen (O) atoms, usually with a hydrogen–oxygen atom ratio of 2:1 (as in water) and thus with the empirical formula (where ''m'' may or may ...

involved in protein

post-translational modification Post-translational modification (PTM) is the covalent and generally enzymatic modification of proteins following protein biosynthesis. This process occurs in the endoplasmic reticulum and the golgi apparatus. Proteins are synthesized by ribosome ...

. It broadly includes (but is not restricted to)

database In computing, a database is an organized collection of data stored and accessed electronically. Small databases can be stored on a file system, while large databases are hosted on computer clusters or cloud storage. The design of databases sp ...

software Software is a set of computer programs and associated documentation and data. This is in contrast to hardware, from which the system is built and which actually performs the work. At the lowest programming level, executable code consists ...

, and

algorithm In mathematics and computer science, an algorithm () is a finite sequence of rigorous instructions, typically used to solve a class of specific Computational problem, problems or to perform a computation. Algorithms are used as specificat ...

development for the study of carbohydrate structures,

glycoconjugates Glycoconjugates are the classification family for carbohydrates – referred to as glycans – which are covalently linked with chemical species such as proteins, peptides, lipids, and other compounds. Glycoconjugates are formed in processes term ...

enzymatic Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products. A ...

carbohydrate

synthesis Synthesis or synthesize may refer to: Science Chemistry and biochemistry *Chemical synthesis, the execution of chemical reactions to form a more complex molecule from chemical precursors ** Organic synthesis, the chemical synthesis of organ ...

and

degradation Degradation may refer to: Science * Degradation (geology), lowering of a fluvial surface by erosion * Degradation (telecommunications), of an electronic signal * Biodegradation of organic substances by living organisms * Environmental degradation ...

, as well as carbohydrate

interactions Interaction is action that occurs between two or more objects, with broad use in philosophy and the sciences. It may refer to: Science * Interaction hypothesis, a theory of second language acquisition * Interaction (statistics) * Interactions o ...

. Conventional usage of the term does not currently include the treatment of carbohydrates from the better-known nutritive aspect.

Issues to consider

Even though

glycosylation Glycosylation is the reaction in which a carbohydrate (or ' glycan'), i.e. a glycosyl donor, is attached to a hydroxyl or other functional group of another molecule (a glycosyl acceptor) in order to form a glycoconjugate. In biology (but not al ...

is the most common form of protein modification, with highly complex carbohydrate structures, the bioinformatics on

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 i ...

is still very poor. 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.Dove A (2001). Nature Biotechnology 19:913-917. http://www.columbia.edu/cu/biology/courses/w3034/LACpapers/bittersweetNatBiot01.pdf Also, the number of

simple sugars Monosaccharides (from Greek ''monos'': single, '' sacchar'': sugar), also called simple sugars, are the simplest forms of sugar and the most basic units (monomers) from which all carbohydrates are built. They are usually colorless, water-solub ...

that make up

glycans The terms glycans and polysaccharides are defined by IUPAC as synonyms meaning "compounds consisting of a large number of monosaccharides linked glycosidically". However, in practice the term glycan may also be used to refer to the carbohydrate p ...

is more than the number of

nucleotides Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules w ...

that make up DNA or RNA. Therefore, it is more computationally expensive to evaluate their structures. One of the main constrains in the glycoinformatics is the difficulty of representing sugars in the sequence form especially due to their branching nature. Owing to the lack of a genetic blue print, carbohydrates do not have a "fixed" sequence. Instead, the sequence is largely determined by the presence of a variety of enzymes, their kinetic differences and variations in the biosynthetic micro-environment of the cells. This increases the complexity of analysis and experimental reproducibility of the carbohydrate structure of interest. It is for this reason that carbohydrates are often considered as the "information poor" molecules.

Databases

Table of major glyco-databases.Egorova K.S., Toukach Ph.V. (2018). Glycoinformatics: bridging isolated islands in the sea of data. Angewandte Chemie International Edition 57:14986-14990 , doi:10.1002/anie.201803576

References

{{Bioinformatics Bioinformatics Carbohydrate chemistry Glycomics