Summary: Where is VirusWorld?
VirusWorld was hosted since its inception at the Institute for Molecular Virology in 1993/1994 at the dawn of the World Wide Web. The site has not been updated since around 2014 and has been retired. However two (mostly complete) archives are available from two separate sources where visitors can find the original images:
|VirusWorld Legacy||VirusWorld Web Archive|
|A “Legacy” version into which images have been reassembled in a responsive web design and grouped by both virus family and virus genus.||Web Archive” version, last copied on April 23, 2022: This archive is housed at The Wayback Machine (web.archive.org) a digital archive of the World Wide Web launched in 2001.|
The VirusWorld Web Archive site pages retain the links that were included at the time. However, while some links still exist, some link to links within the Archive.org gigantic database, while other links are defunct.
The VirusWorld Legacy was constructed with a responsive web framework to facilitate navigation from smart phones or tablets. The site preserves most of all the original images.
These Virusworld archives and legacy sites should satisfy those that are searching for actual images originally used in scientific articles, PhD. theses, news articles etc.
Other virus image sources
In the 80’s and 90’s it required an expensive computer and expertise to create virus images from atomic coordinates that can now be created easily even on a laptop with free software such as UCSF Chimera or ChimeraX, and many other molecular graphics software.
A Short VirusWorld History
This July 2022 week saw the end of VirusWorld. “It” had a good lifespan of about 29 years, which is not bad for a web site!
Today is July 12, 2022, and in 4 days Madison, Wi, USA, will once more host the American Society for Virology meeting (ASV 2022 – archives.) The seed of VirusWorld was planted at a previous ASV meeting in 1993 (10-14 July, University of California, Davis, Davis, California.) I was invited by David Dunigan (archive) to present my work on the molecular graphics of viruses in the session concerning teaching virology. My images were very well received and the many requests that followed demonstrated a strong interest and a real need. To avoid spending an enormous amount of time copying images onto 3.5″ floppy disks that would be mailed by US Post, it became apparent that making the images files available online was a better solution. In 1993 the most popular protocol was via “Anonymous File Transfer Protocol” (ftp.) I therefore created this server on the computer that I was using to create the virus images (a Silicon Graphics Power Series.) An anonymous FTP site is not very friendly or exciting to use. But it all changed the next year.
That same year, 1993, the World Wide Web was officially launched in the public domain on April 30, while the Mosaic web browser to navigate the web was also released in 1993. By 1994 the Netscape Navigator was the most popular browser and the Netscape Communications Corporation offered an educational version of its web (http) server. At that time the Institute for Molecular Virology (IMV) had acquired a new Silicon Graphics computer (Indigo2) to work on virus structures from Cryo Electron Microscopy. VirusWorld became “alive” on this new system now running as a web server. This new web interface provided the means to view images before they were downloaded, place them in pages, add text… this was the “WWW revolution!”
The first computers used for VirusWorld at IMV was the SGI systems that we had called “rhino” as we worked on rhinovirus amongst many others. In 1994 the new SGI computer was called “bioinformatics” but at that time that word was rather obscure for most people. Later web server were the IMV servers for both internal file serving and web hosting.
I created most of the images that were on VirusWorld even though I had come to Wisconsin to learn the “new methods” of “cloning and sequencing” that “Next Gen Sequencing” have now rendered obsolete. In 1988 the IMV purchased an Evans & Sutherland PS/390 computer with its associated MicroVAX from Digital Equipment Corporation that ran the display program FRODO. I was offered to “pilot and run” this system to display virus structures derived from X-Ray crystallography. After about one year, I became aware and used the output of the Vsurf software of Michael Rossmann to create a view of the rhinovirus surface using grid lines. This provided a new insight on the virus structure that now appeared easier to grasp. This was a fantastic advancement in the viral particle visualization that even the crystallographers appreciated. I later modified the grid computation using other software in series (MS, SECTION, SURSPLIN, SURSCOP) followed by a set of awk scripts that I wrote to color-code the surface. But this method was very cumbersome and lengthy, and took many hours (even days!) to create a single image. By then I had also switched to a new molecular graphics software from UCSF: MIDAS-PLUS.
At that time the Protein Data Bank (PDB) coordiante files did not contain the 60 necessary 3×4 rotation matrices to compute all the symmetrical atoms within a virion with icosahedral symmetry from the published X-ray coordinates. Fortunately this is now standard and also nowadays supplemented by the Virus Particle Explorer (viperdb at Scripps.)
In 1994 I saw a presentation of the software GRASP by Anthony Nicholls that made a huge impact of further virus images. Anthony was interested by my request to make his software able to open coordinate files for larger structures beyond the small proteins originally planned for this software. For example, a complete rhinovirus virion would contain about half-a-million non-hydrogen atoms once the icosahedral symmetry is applied. At that time computers were not equipped with the generous amount of memory (RAM) that we have now. From this point it became much easier to create new images, within a 1/2 hour. My most difficult task, usually, was choosing the color scheme!
By the end of the 1990’s it was not longer necessary to create images on expensive, large computers and it became easier to create images on a desktop or even a laptop computer. I even created a series of images for the 8th report on Taxonomy using RASMOL, a simple software that fits on 1/2 a floppy disk! Another “cool” one was Qutemol. I have also used PyMOL on occasion.
Nowadays I rely most often on UCSF Chimera or ChimeraX that offer automated script to construct a virus particle from the icosahedral rotation matrices built-in the PDB coordinate files. (For example see the page on this site: adeno-associated-virus.)
I am grateful for the supportive views of the IMV Faculty along my many years at IMV.
I am also grateful for the work of many crystallographers that produced the early virus structures as well as those working in CryoEM structures.
CHIMERA: Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., and Ferrin, T.E. “UCSF Chimera – A Visualization System for Exploratory Research and Analysis.” J. Comput. Chem. 25(13):1605-1612 (2004). https://doi.org/10.1002/jcc.20084
CHIMERAX: Pettersen EF, Goddard TD, Huang CC, Meng EC, Couch GS, Croll TI, Morris JH, Ferrin TE. Protein Sci. 2021 Jan;30(1):70-82. https://doi.org/10.1002/jcc.20084
FRODO: T.Alwyn Jones, Interactive computer graphics: FRODO, Methods in Enzymology, Academic Press, Volume 115, 1985, Pages 157-171, ISSN 0076-6879, ISBN 9780121820152, https://doi.org/10.1016/0076-6879(85)15014-7.
GRASP: Nicholls A, Sharp KA, Honig B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins. 1991;11(4):281-96. https://doi.org/10.1002/prot.340110407. PMID: 1758883.
MS: Connolly M. L., Solvent-Accessible Surfaces of Proteins and Nucleic Acids. Science. 221 (4612): 709–713. https://www.science.org/doi/10.1126/science.6879170
PyMOL: The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC. https://pymol.org
QUTEMOL: Marco Tarini, Paolo Cignoni, Claudio Montani: Ambient Occlusion and Edge Cueing for Enhancing Real Time Molecular Visualization IEEE Transactions on Visualization and Computer Graphics Volume 12 , Issue 5 , Pages 1237-1244 , 2006 , ISSN:1077-2626 http://dx.doi.org/10.1109/TVCG.2006.115
RASMOL: Roger Sayle and E. James Milner-White. “RasMol: Biomolecular graphics for all”, Trends in Biochemical Sciences (TIBS), September 1995, Vol. 20, No. 9, p. 374. https://doi.org/10.1016/S0968-0004(00)89080-5
SECTION, SURSPLIN, SURSCOP: Nathalie Colloc’h, Jean-Paul Mornon, A new tool for the qualitative and quantitative analysis of protein surfaces using B-spline and density of surface neighborhood, Journal of Molecular Graphics, Volume 8, Issue 3, 1990, Pages 133-140, ISSN 0263-7855, https://doi.org/10.1016/0263-7855(90)80053-I.
VSURF: Rosssmann MG, Palmenberg AC (1988) Conversion of the putative receptor attachment site in picornaviruses. Virology 164, 373-382. https://doi.org/10.1016/0042-6822(88)90550-8
- 1993: anonymous FTP site to disseminate requested images for teaching
- 1994: move to the WWW with a Netscape Educational server.
- The original [hand-coded HTML] design look is no longer available.
- A few exceptions: e.g. What is Netscape?, Sept.19, 1995. “Internet Resources for Molecular Biologists” and “Links to Downloadable Free or Shareware programs” both last modified March 02, 2000. Or perhaps my Rasmol tutorial, last modified March 17, 1999 ]
- 1997: redesigned look by Netconcepts. Web pages fit a 640×480 pixels screen, common at the time.
- URL: http://bioinformatics.bocklabs.wisc.edu/Welcome.html [Last Archive – February 7, 2003]
- 2002: “Aqua” look, site designed with
- 2008. Rewrite in php scripts.
- 2014. End of updates (JYS leaves IMV)
- 2022. July. Hardware server changed. Site taken down.