Thanks, Prof Watowich and Grad Student Malstrom (thread Re: DDDT2: Breaking the Silence? ) for your recent updates on the DDDT2 project. I'm very pleased to read that your team has been very busy preparing for the production free energy calculations that we are or will be running. After not hearing from the team for some time, I had been wondering whether some fundamental problems had been found that would have made proceeding with the calculations pointless, but I'm relieved that that was not so. Here's hoping that we find some useful antiviral compounds.

I have no idea of the fundamental differences between the binding energy calculated by Autodock in Phase 1, and the free energy that we are calculating with Q-Chem in Phase 2. I guess that if this was easy to explain here, you would have done so. ...

Do your findings with the failure of Autodock to reliably identify binders to flaviviridae proteins, and the apparent superiority of Q-Chem calculations, have implications for other screening projects, for FAAH/IADS/HFCC within WCG and also for docking projects outside of WCG?
Have other researchers found these sorts of limitations with the types of calculations that Autodock performs, or are you discovering new principles that could lead to improved methods of screening for drug leads?

Regards - Rick

If you look at The Matrix overview chart you can see the different ''engines'' used. DDDT2 uses CHARMM.

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