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Visualizing hla-aw with protein explorer

Protein Explorer is designed as a user-friendly but fairly full-featured visualizer. It is not as scriptable or as powerful as some other visualizers such as VMD and PyMol, but it is one of the quickest and easiest to get started with. It is used through a web browser, either by accessing it through the Protein Explorer website (via the Quick-Start Protein Explorer link), or as an offline version, downloadable from this page . Both versions require the MDL Chime molecular viewing plugin, which you can download from here (registration required).

As with VMD above, a human leukocyte-associated antigen, HLA-AW (PDB structure ID 2HLA), will be shown in various renditions.

Upon opening, Protein Explorer will load a default molecule and display it (this feature may be disabled via a setting under "preferences" in the lower left frame):

Protein explorer at startup

The interface contains three areas. The frame on the right contains the rendering window, where the molecule is displayed. The lower left frame contains an input box for text commands and a text box that displays general text output from the program: What commands have been executed, what the program is currently doing, etc. The top left frame generally contains the user interface in the form of buttons and links. Its exact contents vary with use.

Clicking on the "PE Site Map" link pops up a window containing Protein Explorer's top-level menu:

Protein explorer site map window

Each option contains a helpful tooltip which can be seen by hovering the mouse cursor over it. "New Molecule" allows the user to load a molecule either directly from the PDBor from the local filesystem. "Reset Session" returns to the default view and rendering style, which can be a useful shortcut. "Quick Views" opens up a menu from which the user canselect how the molecule is rendered.

Once a molecule is loaded, the "Quick Views" menu allows the user to control how it is displayed:

Protein explorer quickviews interface

The "SELECT" pulldown menu allows the user to pick a group of atoms based on their properties, their location, the structural elements in which they are involved, or by directly clicking them.The "DISPLAY" pulldown menu then allows the user to determine the style in which the selected atoms are rendered. Most of the styles available through VMD are also available in Protein Explorer. The "COLOR" pulldown menuallows the user to determine how the atoms are colored. Options include coloring by secondary structure elements, atom type, subunit (chain), a spectrum from end to end of the protein, and by properties such ascharge and polarity.

Protein explorer: hla-aw backbone rendering

This rendering mode shows the protein backbone (no side chains) through the alpha carbons of each amino acid residue. It gives the user a sense of how the chains fold to form the structure, but not it's full shape, since all side chain atoms have been removed. The yellow bars are disulfide bonds, which are covalent bonds that lock distant parts of the chain together to help maintain the structure.

Protein explorer: hla-aw cartoon style

Cartoon rendering works as for VMD. As in the backbone rendering above, side chains are ignored, and the protein backbone is rendered as a smoothly curving tube. Beta sheets appear as flattened arrows, and alpha helices appear as spiraling ribbons.

Protein explorer advanced explorer menu

More advanced rendering methods are available through the Advanced Explorer Menu.

Protein explorer surfaces menu

The Surfaces menu allows the user to display the surface of the protein. Several variable are available, including the radius of the probe used to define the surface, as well as several methods of coloring the surface based onchemical and physical properties.

Protein explorer: hla-aw surface rendering

This rendering style shows the surface of the protein accessible to water. This image is tilted 90 degrees toward the viewer from the previous images.

Protein explorer: hla-aw superimposed images

By setting the surface to be transparent, it is possible to superimpose another rendering style over it, and see how it fits into the surface. This can convey an idea of how the fold of the chain relates to the overall three-dimensional shape of the protein.

  • A detailed introduction to protein structure and function can be found in most introductory biochemistry textbooks. For example, Lehninger Principles of Biochemistry, 4th Edition, by D. L. Nelson and M. Cox (sections 2.1, 3.1-3.5, 4.1-4.4, 5.1-5.3).
  • The Structures of Life at the NIH web site. This site is an introduction to protein structure, structure determination methods, drug design techniques, and other applications of structural biology.
  • Protein Structure and Function , by Gregory A. Petsko and Dagmar Ringe. This book provides an overview of the basic biochemistry of structural biology. Topics covered include protein structure, mechanisms of protein function, regulation of protein function, and case studies of the kinds of problems that arise in structural biology.
  • The MIT Biology Hypertextbook . This online textbook provides introductory level coverage of the field of microbiology. It includes cell biology, protein biochemistry, genetics, metabolism, and molecular biology. New content is typically added over time.
  • Artificial Intelligence and Molecular Biology . This online book includes chapters on classifying protein structures, predicting protein structure, and analyzing crystallographic and NMR data to determine protein structure. Of particular interest to readers of the current page who have a computer science background but need to understand more of the basic underlying biology is Chapter 1: Molecular Biology for Computer Scientists .

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Source:  OpenStax, Geometric methods in structural computational biology. OpenStax CNX. Jun 11, 2007 Download for free at http://cnx.org/content/col10344/1.6
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