JediPlus... hmmm, of course you know that if you bring up the graphics and push the mouse over the main frame, you can play the game of spinning target around at will and create your own view of the docking, or :D

Hello whocrazy,
ZINC means that the work unit is generated from the very large Zinc fragment database. I don't know where the JEDI work unit name came from.

Lawrence

Hi whocrazy,

Kudos for being observant!

JEDI stands for compounds Derived from and/or Inspired by JE-2147 (an active site inhibitor). I suppose it also has something to do with the fact that my middle name is Luke. ;)

There will be many, many more work units that involve different ZINC compounds. The people at the ZINC database provide free, well-formatted copies of several different libraries of ligands from the National Cancer Institute (NCI). The NCI Diversity Set has 1,900 different compounds, and the NCI fragment library has 32,000 different compounds. I dock each library against hundreds of different conformations of the drug target (HIV protease). I also use different strains of the target, such as a wild type/normal version and different multi-drug-resistant mutants of HIV protease (that is, the "superbugs"). And I'm docking compounds to two different regions on all of the targets: the active site (where the current drugs bind) and the potential allosteric inhibitor site (a new, potential target that we are trying to validate as a real drug target).

As for the alphabetic names, I am guessing that you are referring to the compounds that had three-letter names (or x and then three other letters), right? Those are three-letter abbreviations for different FDA-approved HIV protease inhibitors (which all bind to the active site). They are being used as reference compounds, to (1) provide a base-line number against which to compare the performance of other compounds, and (2) to help test and refine the computational methods being used.

Thank you very much for your interest and for your help,
Dr. Alex L. Perryman

Hi sekerob,

That is so cool!!! I just tried the interactive mode for controlling the target's orientation, and I find it very informative. And it's fun, too.

Thanks for the tip,
Dr. Alex Perryman

oh boy. thats just what we need. a mad boffin called luke skywalker. buahahahaha. (jk)
ps: when there is a new work unit downloaded, I like to fire up winrar and view each file of the work unit, IE, like loading up a text file in notepad.
Even though the various numbers and words mean nothing to me, I feel like I am able to get to know the project better by studying each file.
Not too long ago there were these work units with 1 particular file had someone's name and a year IE (1995 or 1993)
You mention docking. How do you actually create these work units. Do you have to manually type them out into a text editor?
it must be a lot of hard work having to type out half a meg worth of numbers, if you get one little thing wrong, the boinc work unit would probably fall over.

faah_protease_5.42.dat
74
60
-9.49359 -21.5189 -4.60563
etc.
once again thanks for explaining how it all works.