- Contents of VIPERdb
- Organization of Images on Info Page
- Using/Extracting the information
- Lattice Types and Matrices
- How to Generate a Complete Virus Particle?
- Contact Us
What is VIPERdb?
VIrus Particle ExploreER (VIPERdb) is a website and (behind the scenes) a curated repository and database of spherical virus structures and their structure derived results. All the virus structures available at the PDB are organized in a standard "VIPER" convention for the ease of their representation and computational analysis. Each virus structure (entry) is pictorially represented in terms of its surface topography and their subunit organization as well their subunit tertiary structures. Also, each entry is analyzed in terms of their subunit-subunit contacts and association energies using the molecular mechanics program CHARMM. Currently, all entries in the database are of non-enveloped icosahedral viruses, but the work in underway to include helical viruses.
How to cite us.
You are free to use any of the information or figures available throughout this site in your work and publications, but please reference VIPERdb by mentioning:
The figures/data were obtained from VIPERdb. (https://viperdb.org) and cite the following reference:
VIPERdb v3. 0: a structure-based data analytics platform for viral capsids.[View article]
Montiel-Garcia, D., Santoyo-Rivera, N., Ho, P., Carrillo-Tripp, M., Johnson, J. E., & Reddy, V. S.
Nucleic Acids Research (2020); doi: 10.1093/nar/gkn1096
About the FAQ.
Any information that we think/find important! We will definitely include more questions that come from users of the VIPERdb site. So please send your questions to email@example.com
This faq is written and maintained by the VIPERdb Team, with input from many current and past VIPERdb members. We are always happy to receive and accommodate any comments/corrections/add-ons. If you have any questions or comments, drop us a line at firstname.lastname@example.org or go to the contact page.
Contents of VIPERdb
How Are Virus Entries Organized on VIPERdb?
The viruses can be grouped by their family, genus or quasi-symmetry/T-number, or whether it was determined by x-ray or cryo-EM
How Are Values/Calculations Determined for Each Entry?
See our explanations page on calculations.
Organization of Images on Info Page
A surface rendering of the virus particle (biodata-lower right/illustrations-left) is generated using the TexMol program based on the atomic coordinates of the viral capsid proteins. The colors are depth cued according to the radius from blue to yellow. Thse renderings appear similar to those of cryo electron miscroscopy reconstructions at 20 Å resolution. The rendered surface representations readily brings out large-scale features such as "peaks" and, "canyons" and distinctive morphological units (e.g. hexamers and pentamers). It is convenient to compare different virus particles with these renderings as these images are generated on a relative scale. Thus it is possible to create a gallery/montage of viruses that are scaled to each other by combining these images with those from other viruses using the Gallary maker utilty.
Ribbon Drawing of the Subunits
A ribbon drawing of the subunit(s) (biodata-top right) is provided for each unique gene product in the viral capsid. For a quasi-equivalent virus made of multiple copies of a single gene product, all the subunits that constitute the icosahedral asymmetric unit are shown (e.g., A, B and C subunits of T=3 capsids). For picornavirus and related capsids there will be three ß-sandwich domains. The ribbon drawings are colored with different tones to distinguish each unique subunit.
Geometric Description of the Capsid
A geometric description of the capsid (illustrations-tab, middle diagram) shown with each virus was found to best describe the geometry of the subunit interactions. All of the viral capsids in this database display icosahedral symmetry. Some of the particles have the shape of an icosahedron, while others resemble other geometric solids that display icosahedral symmetry. These include truncated icosahedron, rhombic triacontahedron and dodecahedron. The fidelity of some viruses to these shapes is remarkable with dihedral angles between subunits conforming to within experimental error to the dihedral angles required to form the geometric solid.
Under the Subunit Organization image (illustrations-tab, right diagram) is a pull-down menu that allows for selection of different views for the capsid rendered using Chimera. This includes various representations corresponding to different resolutions as well as inside view of the capsid, and views with ribbon or tube representations.
On each individual virus/entry page, you will find two images in the (default) biodata tab: 1) ribbon diagram of the subunits (protomers) and surface representation of the entire virus. In the illustration-tab, there are 3 different representations are shown. You may click on each image to pull up the enlarged version of the image in a separate window.
Using/Extracting the Information
How to Save?
In the biodata-tab of each virus info page, there are links to the primary sequence of chains in the IAU, the PDB header file containing contextual info, the pdb to viper transformation matrix used to reorient the pdb coordinates, the transformed PDB coordinates, and coordinates for the full capsid, half capsid, and lattice. Click on any of these and the file will be displayed on the full screen. You may then use the save option on your browser if you would like to download them.
These are from the Protein Data Bank (PDB) site. They contain information about the virus, details about the structure determination amino acid sequence, secondary structure of the subunits etc.
This file contains the matrix which takes the original PDB coordinates (from the PDB databank) and puts them in the standard orientation (Z35X looking down the z-axis).
This file consists of the complete PDB entry, BUT CONTAINS THE TRANSFORMED COORDINATES, which corresponds to the particle at the origin (0,0,0) and placed in the standard orientation. Also co-ordinates of the hetero atoms and water molecules have been reorganized to better suit further analysis using CHARMM.
To save images: (right)click and hold on the image to be saved, you would see options: 1) view image 2) save image as etc., select the save option, a new window would pop up asking for the place to save, give a name with a proper extension that corresponds to the image format.
How to Enlarge?
Click on the any of the images on individual virus pages an enlarged image will pop up in its original size. If further enlargement is desired, you can try the zoom in option on your browser or save the images and view and enlarge them under any graphing programs or image viwers.
How to Compare two or more Images?
Visit the gallery_maker page, in which you can select any number of viruses and perform a side-by-side comparison of them according to their topology (to see relative sizes and surface features), ribbon subunits, capsomeres, or even their crystal contacts in the crystal lattice (available only for few entries).
Where to Find Related Entries of a Virus?
Related entries can be accessed by clicking on the tab on each info-page of a particular virus. For example, if you would like to find mutants or related entries of the bacteriophage MS2, just go directly to bacteriophage MS2 page and click on Related-Viruses tab.
How to search for viruses within family/genus/T-number?
You can search for viruses within family/genus or of a particular T-number, by using the links family-index, Genus-index or T-number index links under the "Data" pull down menu at the top. Then chose choose a family/genus/T-number of interest from the pull down menu at the top.
Specific search: input either virus name, PDB ID or T number and this search engine will bring you directly to the page you want.
General Search: If you don't know the exact information for certain virus or you would not be able to use the specific search engine. Then you can try to use this search engine with partial information (e.g., rhino for human rhino vius entries). It searches on the whole contents of this site and returns the list of links with related topics. From there you can find your way.
Lattice Types and Matrices
Lattice Types and Matrices
Viruses are often categorized by their T-number and P-numbers. The T-number describes the quasi symmetry present in the virus capsid, while the P-number describes the icosahedron's pseudo-symmetry. Follow this link for further information about lattice types. There are sixty icosahedral matrices (Show me all 60!). By applying each of these matrices on the icoshedral asymmetric unit (IAU), complete virus capsids can be generated. Certain matrices from this list of sixty were used to generate capsomeres of virus particles. Please note that these matrices correspond to particles in the standard orientation. You may find the matrices that are required to generate capsomeres found in each of the following T-numbered capsids:
How to Generate a Complete Virus Particle?
Steps to Generate a Complete Virus Particle
Visit the Oligomer Generator and follow the instructions found there, or you can do it manually:
1. Download Transformed Coordinates. 2. Download 60 Matrices. 3. Apply 60 Matrices on Transformed Coordinates.
Have Questions for the Whole VIPERdb Team?
Our email address is email@example.com.