A slideshow on BEDAM, the Binding Energy Distribution Analysis Method http://www.columbia.edu/cu/chemistry/CADD/slides/cadd-01-levy.ppt

Hello Sgt. Joe,

Here's an old post that attempts to explain how BEDAM would fit into our workflow:

https://secure.worldcommunitygrid.org/forums/...ad,36921_offset,10#465401

As far as a layman's explanation of technique, I will try to explain BEDAM in context of docking. Docking (like Vina) attempts to efficiently sample docking poses of a small molecule in a protein surface. These poses are given a score that is based in theory, experimental data, or both. Arguably, the faster docking programs use a semi-empirical (theory and experimental) scoring function. Further, the faster docking programs are grid-based, where the protein is reduced to a smaller set of 3D coordinates to decrease the time of calculating a score. Now, take away everything that I just discussed to have:

Theory-only scoring function
All-atom simulations (no grids)

AND

Only keep track of scores and *not* poses
(Writing coordinates to disk is time-consuming)

And you have BEDAM.

The energy distribution is more accurate (there is probably no accuracy in energy distribution from docked poses), so the score is more accurate.

Thanks for the interest,

Dan

AIDS Cure is what would make companies big cash. it is worth while to keep it running. Sad to say that even WCG has a cash price attached to it.
if not, why previous projects that no cures have been found have stopped. simple, no cash forecast on them.

Oh boy, is this going to be fun... Emilio, please explain the above statement: where does WCG have a "cash price" associated to FAAH?

Thanks,
CJSL

Crunching for a brighter future...

If I may ...
This reminds me of many NASA press briefings in the earlier days of the
Space Shuttle. Some reporter would always ask the Money question about
how much all that research was costing.

Finally, one astronaut, who was heavily involved with microgravity drug
research, explained:
Once the space part of the research is done, showing you what drug
candidates to try, it still takes about another _Decade_, ten more years,
to make some of them, test them in laboratories, run clinical trials,
get government approvals, etc., before you have a marketable drug
that will help people and, yes, make a lot of Money to repay the ten$
to hundred$ of million$ it took to make just one new, safe, effective drug
available.

But sometimes, the number of people in the world who need
a new drug is _not_ enough to recoup their investment. They make
the drug available anyway.