hi, why does nobody answer his question? is it really too difficult for the people in charge of the project to just go once a day on the forum answer a few questions?

The Fight@AIDS@Home scientists are excellent at answering technical questions about their project, so usually we leave questions like this to the experts. It does, however, take a week or so for them to answer.

But from my own limited knowledge, I would say yes - the extra-small work units from experiment 17 should all be complete now.

Hi Larry,

Yes, those batch numbers (i.e., 3202 to 3702) correspond to Experiment 18. This experiment is similar to Experiment 10, but it's targeting every 10th picosecond snapshot from the first 5 nanoseconds (i.e., 500 conformations) of the MD simulation of the V82F/I84V multi-drug-resistant mutant of HIV-1b protease. Experiment 10 just targeted 7 of those conformations (ones that I thought would be useful at resolving compounds that bind well from those that don't, as determined by my previous experiments on this ensemble of conformations). Comparing the results of Experiment 10 to Experiment 18 and to Experiment 19 (which will target a group of conformations selected by a new clustering approach--the QR factorization method, which is part of the VMD package from the Univ. of Illinois, Urbana-Champagne, or UIUC), will help me learn about the best ways for picking the particular snapshots (i.e., shapes or conformations) that I target in these docking calculations. Thus, it's helping me test and refine the methods and strategies that will guide future experiments on HIV protease, and it should also provide useful info. by itself. By sharing the results of testing these different strategies, we can help other scientists in their research against other diseases, as well.

I've asked Dr. Garrett Morris about this, and he will soon update the
http://fightaidsathome.scripps.edu/ page to include the batch numbers with the description of each experiment.

I'm sorry for being so late in my responses here, but my nights and weekends have been very busy for the last month. My cheap studio apartment flooded with sewer water about a month ago. Dealing with that mess, getting the run-around from my landlord, and finding a new place to live have been consuming my nights and weekends (the times during which I normally respond to the FightAIDSatHome Forum).

Thanks for your help,
Dr. Alex Perryman

Thanks Dr. Perryman for the update. I'm always appreciative of the frequent updates that you do provide. I'm sorry with the appartment situation, but with no other way to help I look forward to continue crunching fa@h.

-Lt. Dan.

Hi Larry,

Thank you very much for your advice. After my landlord dragged his feet and then dodged his responsibility, I ended up contacting my renter's insurance people. Allstate treated me very, very well. I already received my check from Allstate, and I used it to help me move into a much nicer 1 bedroom apartment (and to buy a nice, ergonomic couch). I now have much more space, and I'm also much closer to work. I'll get to save ~ 50% on my gasoline bills, and I can now avoid the freeway when I drive to work (i.e., it's a less stressful and much, much safer commute for me now). I'm trying to focus on the positive aspects of this situation. ;)

My renter's insurance agent mentioned that they would probably pursue some type of negligence suit against my former landlords. But, luckily, that's not my problem anymore.

Thank you very much for your concern and for your advice,
Dr. Alex L. Perryman

PS--for all you hardcore, stereotypical nerds out there (such as myself).........................most of the damages from that flooding incident involved the fact that my very rare, 1st edition copies of books and modules for Dungeons and Dragons were destroyed. I lost many collector's items that were actually written by Gary Gygax, himself. Sadly, Gary Gygax died last month. All of us nerds should give him a moment of silent reflection and gratitude.