Bio-Prodict releases a suite of 3DM systems to support COVID-19 drug and vaccine R&D

In view of the COVID-19 pandemic, Bio-Prodict would like to do its part by developing 3DM systems for the SARS-CoV-2 proteins. We will make these systems available free of charge to scientists working on COVID-19.

3DM facilitates many aspects of protein R&D, from protein engineering to drug design and vaccine research. These systems can be a valuable asset to anyone doing research on SARS-CoV-2 proteins. Therefore, we’ve built 3DM systems for several key proteins of the SARS-CoV-2 virus:

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• Main protease

• RNA-dependent RNA polymerase

• Spike glycoprotein 

• Nucleocapsid protein

If you’re a scientist working on SARS-CoV-2 and interested in 3DM, please contact us (mail Henk-Jan Joosten, joosten@bio-prodict.nl) and we will help you set up 3DM and give you access to the systems. We’re also actively looking for collaborations to further develop this COVID-19 3DM suite.

Below you can find a brief overview of 3DM and how it can help you with your research. We’ve also put together a short example analysis of the spike protein with 3DM, which you can find here. 

3DM systems are protein super-family platforms that collect, combine and integrate many different types of protein-related data. They can facilitate protein engineering, drug design, vaccine research and any other protein R&D that requires in-depth knowledge about the molecular mechanisms of a certain protein family. One of the main powers of 3DM is the ability to provide insight in protein residues by transferring data from other members of the protein family onto a protein of interest (sometimes from up to 300 thousand protein sequences) or to visualize this data in any of the protein structures. 

For example in this SARS-CoV-2 main protease sequence, you can see that histidine 41 is a very conserved residue (in 100% of sequences in this family it’s also a histidine), and it has 103 ligand contacts, and many mutations described in the literature - that makes sense because this residue is often bound by different inhibiting compounds. Finding all this information by hand would take you a lot of time and effort, digging through the literature and taking into account the different residue numbers of other protein sequences. 3DM offers you a shortcut - you can get to the important information in a faster, easier way.

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3DM allows you to visualize all sorts of data, e.g. mutations mined from the literature, directly on top of a protein sequence - you can see hundreds of mutations that were described in the literature for a certain residue position across the whole protein family. Selecting a residue will give a detailed overview of that residue, such as its conservation and available literature (of equivalent residues in family members).

Other visualisations include a correlated mutations view, that can give you an idea about evolutionary pressures in the family, or structural contacts - this can be especially helpful if there is no structure available for your protein sequence but there are structures for other proteins in this family. Projected on top of your sequence you can see which residues in the available structures have interactions with a ligand, or for example DNA. It’s simple as that - click on a residue and 3DM will tell you all it knows about it based on the information derived from other proteins in this family.

If you’d like to know more about 3DM and it’s tools, please visit www.bio-prodict.com or contact Henk-Jan Joosten, joosten@bio-prodict.nl.