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Welcome to VIPERdb!!

Welcome to the Virus Particle Explorer, an information source for the analysis of high resolution virus structures. VIPERdb is a one-stop site dedicated to helping users around the world examine the many icosahedral virus structures contained within the Protein Data Bank (PDB) by providing them with an easy to use database containing current data and a variety of analytical tools. Here we will guide you through the main aspects of the VIPERdb website and familiarize you with many of the features it offers.


The Main Menu

In the top of the screen you should see a menu listing the various main sections of this site. When you place your mouse over one of the items on the menu, a submenu should appear, listing the individual subsections. Sections that have an arrow to their right will open a third popup menu with further subsections. If you do not see a menu, then it is possible that you either have javascript disabled, or our javascript is not compatible with your browser. Learn how to enable java by visiting our javascript page.

The Virus Pull Down Menus
In the upper right section of the VIPERdb bar, there are two pull down menus, labeled "Cryo-EM Entries" and "X-ray Entries", which will take you directly to the Virus detail page that you select. Viruses listed under the "Cryo-EM" menu contain structures that have been created based on Cryo Electron Microscopy data, while those under "X-ray Entries" have been constructed through the use of X-ray Crystallography.

The Bottom (Footer) Menu
If you have disabled images or javascript in your browser, you can still access all of our pages through the text-only links at the bottom of every page. Here you can also find links to the Multiscale Modeling Tools for Structural Biology (MMTSB) and The Scripps Research Institute (TSRI) sites.

The virus detail pages sum up all the information about the individual viruses within our database, as well as providing links to downloadable files, publications, and VIPERdb-computed data.
The detail pages are broken up into the following sections:
  • Resume: A listing of the raw data gathered from the virus structure. Here you can find a description of virus properties such as the diameter and symmetry along with links to PDB and Amino Acid sequence entries.
  • Calculations: A collection of the calculations we have performed on the data collected from the virus in order to offer a better description of the virus properties. For more detailed information regarding these calculations, visit the calculations page .
  • Downloads: Links to the header file, the transformation matrix, and the transformed PDB coordinates. The tools offered on this site (such as the oligomer generator) require that the virus coordinates be in a standard orientation (Z35X looking down the z-axis), so here we offer the matrix by which you can convert the PDB coordinates to VIPERdb coordinates, or simply download the transformed PDB file.
  • Graphic Representations: Taking up the majority of the virus detail page are four graphical representations of the virus, each emphasizing a distinct characteristic of its unique structure.
    For a more detailed description of the graphic representations, click here.
    • Topology: This is a surface rendering of the virus particle based on the atomic coordinates of the viral capsid proteins, drawing attention to large-scale features and distinctive morphological units.
    • Geometric Lattice: The quasi/pseudo symmetry present in the virus capsid is represented here by a geometric lattice, helping to better describe the geometry of the subunit interactions.
    • Subunit as Ribbon: This is the unique gene product within the viral capsid represented as a protein ribbon drawing, colored continuously from blue at the N-terminus to red at the C-terminus.
    • Capsomeres: Displayed as a C-alpha strand of the subunits colored by unique chains, this image clearly illustrates the dominant interactions within the particle.
  • Visualization: This section gives any existing methods of further visualizing the virus structure, such as through use of PDB's "QuickPDB", NCBI's "Cn3D" or MDL's "CHIME 2" plugin. For more information concerning these visualization tools, click here.
  • Related Entries: Any related entries such as procapsid structures or mutants of the virus wild-type can be found listed here.

  • The site is being developed as part of the training, service and dissemination component of the NIH Research Resource: Multiscale Modeling Tools for Structural Biology (MMTSB).

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