The global war on error
The Global War on Error is the never-ending struggle for optimal docking.
Olaf Wiest's father says: Speed, Price, Quality. Pick two.
Let's see DOCK Blaster is fast. Check. DOCK Blaster is free. Check. That leaves quality.
The "Global War On Error" also known as the "Never-ending Struggle Against Violent Extrema" is pursuing a cast of unsavory characters wherever they are found.
These molecules appear broken in a docking hit list. Of course, this is simply a problem in our software. You can take these fellows on by telling us about them. We'll send a hit squad out to rebuild them into nice unbroken molecules.
Wrong protonated states
These guys are tricky. Here, we need you to inform us about them when you find them, but also you'll need to explain why they are wrong unless it is really obvious (a short sentence will usually do).
These guys are even more subtle. What makes matters worse is that two sober chemists will often disagree about which tautomer is more physiologically relevant. When you let us know where they guys are hiding, please make a case that includes some sort of documentary evidence so we can bring them to book.
There is a seething underworld of problems in molecular docking in general and our software in particular. A kind of "10 most wanted list", if you will. More will be added here soon. Until then, please help us find these guys and help us "smoke 'em out of the binding site". Your fellow DOCK Blaster users will be grateful.