Visual Molecular Dynamics VMD

Visual Molecular Dynamics VMD

Length: 502 words (1.4 double-spaced pages)

Rating: Excellent

Open Document

Essay Preview

More ↓
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.

How to Cite this Page

MLA Citation:
"Visual Molecular Dynamics VMD." 18 Sep 2019

Need Writing Help?

Get feedback on grammar, clarity, concision and logic instantly.

Check your paper »

Molecular Dynamics And Its Effect On The Proteins Essay examples

- Molecular dynamics (MD) simulation was performed to investigate the site-specific glycosylation effect on the proteins. Model peptide system was galactosylated at different sites in silico, and the conformational characteristics of each glycosylate peptide were analyzed by the MD simulations. Only double-glycosylated peptide showed a structural disruption accompanying a helical splitting, in which Ser17 was particularly weak point to begin destabilization. The MD simulation revealed molecular-level mechanism of the glycosylation effect on the peptide to understand the experimentally observed phenomenon for inhibiting amyloid formation in the model peptide....   [tags: Protein, Amino acid, Glycosylation]

Research Papers
1414 words (4 pages)

Essay about Exploring the Dynamics of a Workgroup

- While participating in the leadership program team members are given a project to complete during their internship. This assignment is in addition to the other work responsibilities they are performing. The team is composed of team leaders and followers. The objective is to gain experience in working with teams, workgroup dynamics, exposure to other work, and skills. The stakeholders select the project and the project team leaders keep the project owners apprised of its progress. Topics selected usually benefit the organization....   [tags: Group Dynamics]

Research Papers
1196 words (3.4 pages)

A Study On Molecular Diagnostics Essay

- Chandni Shiwbodh Molecular Diagnostics Molecular Diagnostics is defined as tests which identify certain patterns in both RNA and DNA. These tests are able to identify RNA, genes, and protein sequences which play a role in diseases. These sequences may be linked to diseases which include nucleotide polymorphism, deletions, rearrangements, and many more. Molecular Diagnostics is also able to identify and multiply the presence of certain microorganisms and cells. Molecular Diagnostics provides a great amount of clinical information....   [tags: DNA, Mutation, Molecular biology]

Research Papers
1724 words (4.9 pages)

Reflective Group Dynamics Essay

- Each individual is categorized into a group from the day they were conceived. According to Kozier et al (2010) a group is “two are more people who have shared need and goals, who taken each other in account in their and who, thus, are held together and set apart from others by virtue of their interaction” (p. 400). The communicate that takes place between members of the group is group dynamic (Kozier et al, 2010). Motivation for participation and similarity of other group members and the goals of the group will affect the group dynamic (Kozier et al, 2010)....   [tags: Group Dynamics]

Research Papers
967 words (2.8 pages)

Molecular Biology And Expressing Gfp Essays

- November 14, 2016 Abigail Lammers Molecular Biology Marion Kawar Introduction: This lab dealt with molecular biology and expressing GFP in bacterial cells. Most of the lab dealt with plasmids. Plasmids are short, circular pieces of DNA that can be used to transmit genetic information into a host cell (for example: adding a gene that will make the host cell glow). These DNA pieces are separate from the rest of the genome and are replicated separately as well. Plasmids join to a DNA sequence through bacterial transformation....   [tags: DNA, Bacteria, Gene, Molecular biology]

Research Papers
2102 words (6 pages)

The Assessment That Is Important For Children With A Visual Representation Of The Family Dynamics And Interactions With One

- The assessment that is most likely to follow from BFT is a genogram. The genogram will provide the family with a visual representation of the family dynamics and interactions with one another. The interventions used will be the process questions along with the genogram. The process questions will assist the family members reflect on their answers, reduce anxiety, and begin accepting their role in the problem. In regards to SFT, the assessment that is most likely to follow is goal setting. Prior to developing the goal, I will facilitate a discussion about the problem....   [tags: Family, Family therapy, Goal, Limitations]

Research Papers
707 words (2 pages)

Essay on Visual Arts : Visual Art

- “Human beings intuit, symbolize, think, and express themselves through dance, music, theatre, and visual art” (Bynoe, Colby 2011). In a future I plan to inspire children and youth, especially my students to love and appreciate the arts. As a future teacher, I will integrate all the VAPA (Visual and Performing Arts) to make the lessons more interesting and to benefit the students. One of the major VAPA I am taking into consideration to use in my future career is visual art. Visual Art could benefit students by improving thinking, accessing emotion, processing information and healing trauma (Bynoe, Colby 2011)....   [tags: Art, Visual arts, Work of art, Arts]

Research Papers
1187 words (3.4 pages)

Masters Program With The Department Of Molecular Genetics Essay

- Attn: Graduate Admissions Committee I am applying to the masters program with the department of molecular genetics in 2016/17 at University of Toronto with the intention of continuing to PhD study. After earning a BSc. in molecular biomedical sciences from HKUST, I worked as a full time research assistant for two years. From conducting independent scientific inquiries, I not only learned and practiced a wide range of molecular biology techniques, but also honed my skills in literature research and review, experiment design, data analysis and critical thinking....   [tags: Molecular biology, DNA, Gene, Gene expression]

Research Papers
936 words (2.7 pages)

Essay on Team Dynamics

- Team Dynamics is how a group of two or more that works together for a common goal. One definition of a team is: two or more individuals associated in some joint action. (Webster’s New Collegiate Dictionary (1976). In the business & education world, these joint actions should have some mission or objective that achieves results like a research paper. My Team C has come together with a common goal: Writing a successful paper for week 5 on “What safeguards exist currently to ensure academic honesty & are they working?” For this to be possible we must learn how to work as a team....   [tags: Team Dynamics Teamwork]

Free Essays
740 words (2.1 pages)

Essay about The Visual Rhetoric of Traumatic Histories

- The Visual Rhetoric of Traumatic Histories Among the problematics that guide my understanding of the possibility of visual rhetorics are three. Each might be considered to exists within/bring together the nexus of history, images, and power. This nexus helps to form a framework for an economy of verbal and visual images that, in turn, might become the fabric of a visual rhetorics. The first is what I want to call the "enigma of unrepresentability." The second is that images become especially important for us when they can be read as "self-reflexive." Finally, the third, is the "ideological privileging" of the visual that renders its apparatus, quite literally, hard to "see." Let me briefly...   [tags: Visual Rhetoric Essays]

Research Papers
1111 words (3.2 pages)

VMD is an important tool in science not only for individuals at primary stage of scientific education, but also individuals who are at a higher level can use VMD to display their ideas and justification concerning a certain topic. With all these creational facilities VMD enables researchers to formulate, and examine almost any desired molecular structure, thus bringing molecular science to everyone’s eyes.
Return to