Molecular Representations

BioCodeKb - Bioinformatics Knowledgebase

The primary purpose of molecular visualization is to support our understanding of the rich, complex material world, by making molecular structures, their properties, and their interactions intelligible.

There are many methods that represent some of the most common models used to represent molecules, but they are not the only models used by scientists. Some models are highly specialized and are used by certain types of scientists. For example, biochemists and biologists use a modeling system called ribbon protein modeling to represent large and complex molecules called proteins.

Although more representative of the actual structure of a compound, stereochemical structures are often difficult to draw quickly. An alternative method of depicting structures with tetrahedral carbon centers relies on the use of Fischer projections. In this, the bonds to the central carbon are represented by horizontal and vertical lines from the substituent atoms to the carbon atom, which is assumed to be at the center of the cross. By convention, the horizontal bonds are assumed to project out of the page toward the viewer, whereas the vertical bonds are assumed to project into the page away from the viewer.

Space-filling models

The space-filling models are the most realistic. The size and position of an atom in a space-filling model are determined by its bonding properties and van der Waals radius, or contact distance (Section 1.3.1). A van der Waals radius describes how closely two atoms can approach each other when they are not linked by a covalent bond. The colors of the model are set by convention.

Ball-and-stick models

Ball-and-stick models are not as realistic as space-filling models, because the atoms are depicted as spheres of radii smaller than their van der Waals radii. However, the bonding arrangement is easier to see because the bonds are explicitly represented as sticks. In an illustration, the taper of a stick, representing parallax, tells which of a pair of bonded atoms is closer to the reader. A ball-and-stick model shows a complex structure more clearly than a space-filling model does. Particular atoms are associated with different colors, for example, black is usually used to represent carbon and white to represent hydrogen.

Skeletal models

An even simpler image is achieved with a skeletal model, which shows only the molecular framework. In skeletal models, atoms are not shown explicitly. Rather, their positions are implied by the junctions and ends of bonds. Skeletal models are frequently used to depict larger, more complex structures.

Ribbon diagrams

These diagrams are highly schematic and most commonly used to accent a few dramatic aspects of protein structure, such as the α helix (a coiled ribbon), the β strand (a broad arrow), and loops (simple lines), so as to give and show simple and clear views of the folding patterns of proteins.

Lewis dot structures are two-dimensional representations of molecules that illustrate each atom as its chemical symbol. Lines indicate bonds to other atoms, and non-bonding electrons are represented as small dots next to the chemical symbols.

Bond-line notation shows selected atoms as their chemical symbols while depicting some carbon atoms as corners between lines and omitting hydrogen atoms that are assumed to be in the structure. Bond-line notation is predominantly used in organic chemistry (chemistry associated with living things).

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