2020-12-04: progress report

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Profile Natalia
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Message 213 - Posted: 4 Dec 2020, 18:18:08 UTC

Hello everyone!

Here is an overview of the work done so far.

Firstly, we have docked 48% of the ligands database to the first target, 3CL Pro. 480 million small molecules were tested in silico. This is a great job! Now we move on to cover 100% of the database.
Virtual screening is a complex procedure that includes post-processing of results, some of them redundant. So the next important step will be processing of the results and studying the chemical subspace they represent. It is important to understand how are the docking scores divided in the dataset. Then our team will develop more efficient filtering rules.

Secondly, the next target for docking is being prepared. Overall, there are 59 targets related to SARS-CoV-2 to investigate.

Thirdly, the new docking software CurieMarieDock has been developed as a fork of RxDock. It is optimised and runs faster. Windows, MacOS and Linux versions are released. ARM version is being prepared.

It is fascinating to work with all of you! Thank you for participating! Have a nice weekend.

With best wishes,
Natalia
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Philip C Swift [Gridcoin]

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Message 320 - Posted: 20 Dec 2020, 20:48:38 UTC - in response to Message 213.  

Hi Natalia

What language is this you speak? Ligands, in silico, chemical subspace representations? Time to swot up. Can I ask about the media's use of the term 'strain' in relation to this beasty adapting itself or being forced to re-adapt.

Thank you for increasing efficiency of filtering rules as it will help people more quickly.

P
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Jim1348

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Message 321 - Posted: 20 Dec 2020, 21:30:01 UTC - in response to Message 320.  

What language is this you speak? Ligands, in silico, chemical subspace representations? Time to swot up.

That is what you will see on Folding, Rosetta and others in the field. Time to upgrade.
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Aurel

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Message 324 - Posted: 20 Dec 2020, 23:42:26 UTC - in response to Message 320.  

I will help you getting an explanation.

An Ligand is an ion or molecule (functional group) that binds to a central metal atom to form a coordination complex. The bonding with the metal generally involves formal donation of one or more of the ligand's electron pairs. (Source: Wikipedia)

in silico means (of scientific experiments or research) conducted or produced by means of computer modelling or computer simulation.

An for the last one
Chemical subspaces are defined by the elements included and the size of the largest molecules. ... A complete chemical subspace is defined as a set of molecules, where breaking any bond in any molecule creates fragments that are also part of the subspace

This topic is a bit harder to explain, however try googling "Systematic Enumeration of Elementary Reaction Steps in Surface Catalysis" to find an short explanation.
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Philip C Swift [Gridcoin]

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Message 353 - Posted: 26 Dec 2020, 23:24:56 UTC - in response to Message 324.  

Thank you :-)
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Philip C Swift [Gridcoin]

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Message 354 - Posted: 26 Dec 2020, 23:26:55 UTC - in response to Message 321.  

Hi Jim

Excuse my ignorance, but upgrade to what? A Hadron Collider? ;-)

P
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Jim1348

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Message 355 - Posted: 27 Dec 2020, 2:20:13 UTC - in response to Message 354.  
Last modified: 27 Dec 2020, 3:03:17 UTC

Excuse my ignorance, but upgrade to what? A Hadron Collider? ;-)

I am not sure what they are working on, but a brainwave accelerator would be useful for all of us. (But the terminology is common on these projects).
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Crystal Pellet

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Message 388 - Posted: 8 Jan 2021, 8:46:48 UTC

Thanks for updating the Research progress on the server status page

Target: corona_3CLpro_v3 (%)	99.997
Target: corona_PLpro_v1 (%)	26.756
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Message boards : News : 2020-12-04: progress report

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