Visual Molecular Dynamics VMD :: Computer Programs

VMD or Visual Molecular Dynamics is a computer program that can be used to design, animate, and model molecules especially organic molecules so that they can be visualized in 3-dimensional graphics for analysis and better understanding of their molecular structure and components. For the most part VMD is used to view and analyze the molecular stimulations, but the program also contains rendering tools that can be used to modify the dimensional and sequential data of the molecules. The data can be applied in various ways. Biochemists can rearrange and form amino acids to observe mutagenesis or functions of the proteins, it can also be useful to predict and understand catalytic mechanisms stimulated by proteins. VMD can be useful to a range of audience, molecular structural data obtained from VMD can be integrated with bioinformatics, which will then provide useful information to researchers of biological system, not only individuals involved with the field of biological science, but also theoretical and experimental researchers of chemical science can utilize the information to scrutinize the chemical structure of molecules. It can also be used in educational institutions to display molecules in a very descriptive manner to students, to give them a broader idea of the structural function. On the organic level VMD is most likely used to model proteins, nucleic acids, and lipid bi-layer assemblies, VMD can also read Protein Data Bank (PDB) files so any protein structures can be found in the VMD database, VMD can create very detailed graphic of molecular dynamics stimulation, then using the variety of tools that are included in the program structures of these organic molecules are then modified and analyzed to view the experimental molecule. One of the major molecule structure created and analyzed in VMD by biologists is the molecule of hemoglobin. Hemoglobin is an essential element of an animal body, iron containing oxygen transport protein in red blood cells, it transports oxygen from lungs to the rest of the body of animals, so it can be used by cells. Hemoglobin plays a significant role in function of an organism, likewise deficiency of hemoglobin causes severe damage to the body. So modeling, and animating hemoglobin molecule structure in 3-D graphics, the diseases and problems caused by decrease of hemoglobin can be discussed and explored more thoroughly, for cure or other diseases that can be caused from the absence of sufficient hemoglobin in the body. The molecular dynamic stimulations of hemoglobin can illustrate the mutations in the genes of hemoglobin proteins, which then can be examined, and modified in order to study the cause, also to predict future possible mutation in hemoglobin genes and their effect.