Personally, I haven't seen any WU in stage 2 of FAAH with a minimum docking energy lower than -11. In stage 1, and in particular 1.b the WU I was getting had a minimum docking energy lower than -10, and the lowest one I remember was -25.

Hello SP88712,
When 2 compunds bind together, they give off energy. To break them apart, you have to add that binding energy back. We want to find a compound that binds very tightly to the HIV protease molecule. Which means that they combine and release a lot of energy. So we start with 2 separate molecules and call that starting state the 0 energy state. If they bind to each other and release energy, we call the energy released a negative energy. That is just because we have arbitrarily named the high-energy state in which both molecules are free the 0 energy state.

Lawrence

Hello SP88712,
This goes far beyond what I am certain of. The official explanation is here: http://www.worldcommunitygrid.org/projects_sh...Faq.do?shortName=faah#197
I can wave my hands and mumble that the side chains on the back bone of the protease molecule are flexible so we have a tremendous combinatorial problem trying to bind two compounds together while taking into account various degrees of freedom for all the atoms. The program shows what it is currently working on and the best that it has done. The 'best' is usually a more negative number than the current numbers, but with the tremendous number of possibilities to check, I just stare blankly into the distance when someone asks me how the algorithm moves through the problem space. I just don't know.

Lawrence