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What is Molecular Graphics?

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  • Written By: Mary Elizabeth
  • Edited By: Bronwyn Harris
  • Last Modified Date: 26 August 2016
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The term graphics refers to drawings or images that are created following rules of mathematics. Molecular refers to molecules and their components. Therefore, one meaning of molecular graphics (MG) is the study of molecules through visualization of the molecules themselves and their component parts. Molecular graphics also refers to the three-dimensional depictions of molecules that are made in order to examine them and understand their responses during reactions and interactions

Molecular graphics have certain advantages over physical models. Physical models can cause problems because the structure is obscured, there is a false impression of flexibility, superimposition is nearly impossible, or they are simply too cumbersome to work with. All of these problems can be overcome with computer graphics.

One key use of molecular graphics is in the study of proteins and nucleic acids. The Research Collaboratory for Structural Bioinformatics (RCSB) protein data bank (PDB), in which experimentally-determined information about the structures of nucleic acids, proteins, and complex assemblies are stored for general access. As of 27 April 2010, there were 64,932 structures in the database. The RCSB popularizes their function with an invitation to visitors to build 3D virus models at Rutgers University on Rutgers Day. The RCSB also sponsors protein modeling trials at regional Science Olympiads in the United States. The Worldwide Protein Data Bank (wwPDB) is the international organization to which groups like RCSB; PDBe, the European counterpart; and PDBj, the Japanese counterpart; belong.

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Another area in which molecular graphics is extremely important is the design of pharmaceuticals. Molecular-graphics assisted drug design — also known as computer-assisted drug design (CADD), computer-assisted molecular design (CAMD), or structure-based drug design (SBDD) — is one of the key research interests of faculty involved in the Virginia Commonwealth University Medicinal Chemistry specialization in the Pharmaceutical Sciences graduate programs, for example.

Specialized software to create molecular graphics, called molecular design software, is available in a number of commercial packages. There are particular versions devoted to molecular-graphics based drug design, as well. In drug design, the feature of docking—the ability to connect a displayed molecule to a receptor—is one of the key attributes that distinguished the drug design software form other molecular design software.

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