Greetings.
I have just joined SiDock and am crunching away...
I like the website - it give approaches to solving COVID infections.

My curiosity:
How do the SiDock WU compare with those of other projects? Such as:
- World Community Grid - Open Pandemics (Scripps Research)
- Rosetta

Thanks in advance!!
Jay

Hi Jay!

You are welcome to the project SiDock@home!

Let me describe the difference between the projects. Just like WCG - Open Pandemics, in SiDock@home we perform virtual screening over a database of small molecules. Each WU performs molecular docking of a small part of the library against a specified target. Targets are various proteins of SARS-CoV-2. However, the molecular docking software is different (AutoDock Vina in WCG, CmDock in SiDock@home, both open-source and actively developing). The sets of targets are also different but can be partly intersecting because the scientific community prioritises some of them as the most important. The databases of small molecules are also different because each scientific group compiles them based on their previous experience.

In Rosetta@home, the scientists analyse the folded proteins, including those of SARS-CoV-2. They also perform protein-protein docking, which means they explore how specially designed proteins dock to the target proteins. As far as I know, they also molecular docking but, again, for different targets, software and the database of small molecules.

I hope it explains the difference between the projects.

I have done all of those projects to some considerable degree, and they are all backed by very capable scientists.
To make a long story short, at the moment I am doing SiDock. I like their considered choice of targets, which is a large part of the puzzle.

And the other reason is a bit negative. After many years of crunching on various docking projects, I have really not seen any of them yield a useful treatment. Since SiDock is new to the distributed computing world, I think they should be given a chance to see what they can do. The best of luck to them.

Thanks to you both for your responses!
Jay

And the other reason is a bit negative. After many years of crunching on various docking projects, I have really not seen any of them yield a useful treatment. Since SiDock is new to the distributed computing world, I think they should be given a chance to see what they can do. The best of luck to them.

They may not have directly yielded a treatment, but they may have eliminated things so other scientists have a better idea what to work on.

I've just received some 3clpro addons, looks like a bonus bit to finish it off? So I shoved 84 cores onto it :-)

Yeah I know my credit is zero, I'm connected through a Gridcoin pool. It pays for the hardware.

Hello Peter!

After additional verification of received results, we saw that some ligands are not processed properly due to the way they were recorded into workunits. We extracted these ligands (about ~0.2% of entire set) into separate work units and generate it for some targets. Also we plan to perform a fix for affected workunits.