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Feb
24

Illustrating and Homology Modeling the Proteins of the Zika Virus

After a busy few weeks of using every bit of spare time and engaging some great and very generous collaborators we now have the latest installment in the #ZikaOpen project submitted to F1000Research. The preprint is also posted on Figshare. The project kicked off after the illustrator John Liebler got in touch as he wanted to illustrate the Zika virus. This really nudged me – or more politely kicked me in the rear, because if we could model the glycoprotein E on the surface of the virion then why not do all the rest of the proteins. It took a weekend of heavy SWISS-MODEL use (summarized here) to produce the files and some further effort to analyze the structures. Again what started as a very simple idea of a ‘research note’ around the Zika virus models expanded to comparing the virions of flaviviruses and predicting glycosylation sites. We used GoogleDocs again to draft the paper over a week or so and as different collaborators connected I would share the draft. This was supplemented with tweets, direct messages, emails, phone calls and Skypes with different team members. Yesterday was the big push and it was polished up this morning. Hopefully this is a significant contribution that others can take and use for docking and screening etc. A MASSIVE thank you to all the contributors especially Carolina Andrade and Bruno Junior Neves in Brazil, as well as all the people who have been acknowledged for supporting this nascent effort. Which brings me to the question – what can we do next? Certainly docking into the valid structures is a priority but if others would like to get in touch please email, tweet, phone etc. John’s Email lead to this you could push us in new directions! Perhaps some funding would help (and that for us is a priority in order to fund the testing of compounds etc) and it is encouraging that several funding agencies have issued Zika virus targeted announcements.  But again the process is likely not fast enough.

Citizen scientists can get involved – but as I found doing the homology modeling not all of the NIH and NSF funded tools and papers are readily accessible unless you have an academic email / affiliation and library access. For me this has to change. Here we are putting our free time into this effort and we have to dig to find the few tools that are accessible. Fortunately I have access also to some commercial software and access to a university library which I am grateful! But still these are important challenges.

I think the big take away here is that you can do quite a bit with a small team contributing in a distributed manner. I am excited and also humbled to be around such great people!

4 comments

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  1. Stacey Arnesen says:

    Some publishers are providing free access to zika-related research. See a list at https://sis.nlm.nih.gov/dimrc/zikavirus.html#a5 as well as several searches of the freely available journal literature from PubMed and the non-journal literature (guidelines, reports, etc) from Disaster Lit: https://sis.nlm.nih.gov/dimrc/zikavirus.html#a6

    1. sean says:

      Agreed some are but not all – please see earlier post http://www.collabchem.com/2016/02/19/zika-virus-insights-from-old-papers-when-you-can-get-them/ and they are not making articles on related viruses open.. There are fewer than a few hundred papers after all. It would not kill them to open up Dengue, Yellow fever articles etc..

  2. Stacey Arnesen says:

    Have you checked PubMed? See the second link above. About a third of the Zika articles in English and listed in PubMed are available for free and about half the dengue articles are free – dating back to the 1800s! They are made available through a companion system called PubMed Central. These don’t seem to be highlighted by the publishers.

  3. sean says:

    half the articles is not enough in my opinion – they should all be accessible.

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