Related Experiment Video
Updated: Mar 19, 2026
09:56
Hierarchical and Programmable One-Pot Oligosaccharide Synthesis
Published on: September 6, 2019
7.3K
CarbBuilder: Software for building molecular models of complex oligo- and polysaccharide structures
Michelle M Kuttel1, Jonas Ståhle2, Göran Widmalm2
1Department of Computer Science, University of Cape Town, Cape Town, 7701, South Africa.
Journal of Computational Chemistry
|June 19, 2016
Summary
CarbBuilder software creates 3D carbohydrate models from text. Version 2.0 enhances modeling of complex polysaccharides and monosaccharides with advanced algorithms for exploring conformations.
Area of Science:
- Computational chemistry
- Glycoscience
- Bioinformatics
Background:
- Carbohydrate structures are complex and diverse.
- Accurate 3D modeling is crucial for understanding carbohydrate function.
- Existing tools may lack comprehensive features for diverse carbohydrate structures.
Purpose of the Study:
- To introduce CarbBuilder version 2.0, a software tool for generating 3D molecular models of carbohydrates.
- To showcase the software's capability in modeling a wide range of carbohydrate structures, from simple monosaccharides to complex branched polysaccharides.
- To highlight the improved building algorithm for exploring conformational possibilities.
Main Methods:
- Development of a portable software tool, CarbBuilder, utilizing text-based input for primary carbohydrate structures.
- Implementation of an advanced building algorithm to explore conformational landscapes of carbohydrate molecules.
- Testing and demonstration using complex polysaccharide models to validate software capabilities.
Main Results:
- CarbBuilder 2.0 successfully generates diverse 3D carbohydrate models, including mammalian and bacterial monosaccharides with various substituents.
- The software's sophisticated algorithm effectively explores a range of possible conformations for specified carbohydrate molecules.
- Illustrative examples demonstrate the accurate modeling of complex polysaccharides.
Conclusions:
- CarbBuilder 2.0 is a versatile and powerful tool for the 3D molecular modeling of carbohydrates.
- The software facilitates research in glycoscience by providing accessible and accurate structural representations.
- CarbBuilder is freely available, promoting its adoption and use in the scientific community.
Related Concept Videos
02:00Molecular Models
45.2K
Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
45.2K
01:24Oligosaccharide Assembly
3.8K
Protein glycosylation starts in the ER lumen and continues in the Golgi apparatus. Glycosyltransferases catalyze the addition of sugar molecules or glycosylation of proteins. Usually, these enzymes add sugars to the hydroxyl groups of selected serine or threonine residues to form O-linked glycans or the amino groups of asparagine residues to form N-linked glycans. Different positions on the same polypeptide chain can contain differently linked glycans.
Multiple sugar molecules that may or may...
Multiple sugar molecules that may or may...
3.8K
01:18Molecular Shapes
63.2K
Molecules have characteristic shapes that are crucial for their function. The arrangement of various electron groups around the central atom dictates their molecular geometry. Electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between the electron pairs by maximizing the distance between them. The valence electrons form either bonding pairs, located primarily between bonded atoms, or lone pairs.
Two regions of electron density in a diatomic...
Two regions of electron density in a diatomic...
63.2K
01:26Biosynthesis of Polysaccharides
855
Polysaccharides such as glycogen and starch are synthesized from nucleoside diphosphate sugars, primarily uridine diphosphate glucose (UDPG) and adenosine diphosphate glucose (ADPG). These activated glucose donors act as key intermediates in carbohydrate metabolism and biosynthesis. UDPG primarily involves glycogen synthesis in animals and many bacteria, while ADPG plays a fundamental role in starch synthesis in plants and certain bacteria.UDPG is formed when glucose-1-phosphate reacts with...
855
03:25Chemistry of Carbohydrates
93.0K
Carbohydrates are an essential part of the diet in humans and animals. Grains, fruits, and vegetables are natural sources of carbohydrates that provide energy to the body, particularly through glucose, a simple sugar that is a component of starch and an ingredient in many staple foods. The stoichiometric formula (CH2O)n, where n is the number of carbons in the molecule represents carbohydrates. In other words, the ratio of carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. This...
93.0K
02:18Fischer Projections
17.6K
Learning to draw Fischer projections of molecules and understanding their relevance plays a crucial role in the visual depiction of organic molecules. A Fischer projection is a two-dimensional projection on a planar surface to simplify the three-dimensional wedge–dash representation of molecules. This is especially helpful in the case of molecules with multiple chiral centers that can be difficult to draw. Here, all the bonds of interest are represented as horizontal or vertical lines. While...
17.6K