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Welcome to VIPERdb!!


Introduction to VIPERdb

Welcome to the Virus Particle Explorer database (VIPERdb), a curated repository of icosahedral virus structures and their structure derived results. At VIPERdb, all the icosahedral virus structures available at the Protein Data Bank (PDB) as well as some user dervied model structures are organized in a single icosahedral VIPER convention. Additionally, each virus structure is analyzed and the structure derived results (e.g., protein-protein interactions, surface accessible residues etc.,) and virus related information such as virus taxonomy and sequence information are stored in a MySQL database. This information can be accessed using various utilities availbale through VIPERdb. Here we guide you through main aspects of the VIPERdb website and familiarize you with the information content it offers.


NAVIGATING THROUGH VIPERdb

Find a Virus
If you know the PDB-ID of the virus that you are looking for, simply enter it into the "Enter PDBID" searchbar. If you don't know the the PDB-ID, then click on "Find a Virus" link and enter the name of the virus that you are looking for. This will take you to the VIPER info_page of the corresponding virus.
The Data Menu
At the top of the homepage you should see various menus. When you "mouse over" the heading of the menu, a submenu appears listing the individual subsections. Sections that have an arrow to their right will open another popup menu with further subsections. If you do not see these sub-menus, then it is possible that you either have javascript not enabled, or our javascript is not compatible with your browser. To learn how to enable javascript, please visit our javascript page. Alternatively, simply click on the name (heading) of the menu e.g., Data or Uilities that should take you to a separate webpage from which you can access the respective links.
The Utilities Menu
By mousing over the heading/title of the Utilities menu, you get to see various utilities that are available at VIPERdb.
  • Submit to VIPERdb: Where you can submit the user coordinates for VIPER analysis.
  • Web API: Where you can access a number API scripts that perform various tasks. [toggle help] provide the syntax how to use the particular API and [run] would execute the script with default parameters.
  • DataBase Browser: Lists various tables that are avilable in the database. Clicking on the tables provides the various parameters stored in the database.
  • Family Association Energies: Lists the table of association association energies at the equivalent interfaces within a chosen family. These lists will be useful to show how the subunit energies are conserved at a particular interface. For example in the case of simple viruses such as Parvoviridae or Bromoviridae.
  • Oligomer Generator: Generates oligomer of interest (e.g., pentamer or hexamer) or a complete capsid of a given capsid that is in the database or on user uploaded coordinates (should be in the VIPER convention). For further instructions please see the README Document
  • Icosahedral Server: A stand alone Utility Developed by Chunxu Qu, Gabe Lander and Jack Johnson that provides the description of different T-numbered lattices and how to generate a particular T-numbered paper model. A great educational utility.
  • Map a Residue: Maps a particular residue on the subunit ribbon diagram (tertiary structure) that can be downloaded.
  • Virosphere: A cool utility that locates the structurally characterized virus families on the Viroshpere.
  • Gallery Maker: A utility that allows you make gallery protraits of all the viruses in a family or selected group of viruses.
  • Contract Finder: A cool utility that lets search for a particular contact between two amino acid residues (e.g., Asp-Arg) within a certain distance in particular virus or a family of viruses.
  • Lattic Matrices: Provides you with a list of rotational matrices that can be used to generate a particular oligomer of interest.
  • Amino acid Information: Another cool utility provides with all the annotation of a particular residue in a virus. For example whether or not it is a surface residue or an interface residue, what are the neighboring residues that it interacts with etc.,
  • Secondary Structure Prediction: Calculates secondary structure based on the 3D structure of the capsid proteins using the STRID algorithm.

  • VPERdb Info_Pages
    The info_pages provide various information about the individual viruses stored in our database. The information is neatly organized in individual tabs on the left
    Biodata: This tab provides the basic information about the entry from the name of the entry, Virus Taxonomy, T-number, links to various data bases, VIPER coordinates etc.,
    Illustrations: This tab provides various graphical representation of the virus created using TexMol, Molscript and Chimera programs. One can choose the images at various resolutionw from the the pull down menu under the "Subunit Organization".
    For a more detailed description of the graphical representations, click here.
    Fold-a-Virus: The tab provides an image of the Flattened Icosahedron of the corresponding Virus (created by Tom Goddard of the UCSF-Chimera team). This image can be saved or opened in a separate window/tab and printed and folded into a paper model
    3D I.A.U. : The tab lets you interact with the icosahedral asymmetric unit of the virus-capsid using the JSmol plugin. Use the mouse to rotate or zoom in/out of the model. The menu on the right provies various JSmol control features.
    CapsidMaps: This cool utility maps the structure-derived information such as interface/core/surface residues using the Google Maps API. Please read the paper by Carrillo-Tripp et al, Journal of Structural Biology, 190, 47-55 (2015) for full description.
    Annotations: Provides a number of structure derived information and annotations. For more information how this information derived, please visit the calculations page .
    Related Viruses: This tab lists the related viruses grouped by Family and by Genus




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