interesting. thanks for the information.

Hi Sekerob,

so you think this means there are no autodock 4 workunits out there yet? In case there are. Do they look different or how would we notice that we have an Autodock 4 unit.

Will these be faster in calculations or will the results be better with Autodock 4?

any idea?

Quite interessted.

Additionally... what will come up on projects. As everything is almost finished, will we only look at Fight Aids and Protenome folding or will there be something new?

For Progress update... I am also very keen on it and think it is not nice from the scientists to leave us in the dark.

Hi Demon999,
AutoDock 4 is the version that has flexible sidechains. When a molecule docks with the target, the sidechains on the target can flex. It makes a difference.

We started FAAH shortly after version 4 was released in 2005. The Molecular Graphics Lab at Scripps has had 2 years to improve the code, so we will be using the 2007 version. We have already run one short Beta test, finding some problems to fix.

Once we have it working for FAAH, we shall use AutoDock 4 (2007) for the first phase of the Dengue Fever project, screening anti-viral compounds. There will be a second phase which will screen the drug candidates that make it through Phase 1 using a different, more computationally intensive program. Then the compounds that make it through Phase 2 will get some lab testing.

We currently expect to bring up a Cancer project after we get Dengue Fever Phase 1 running.

Timing depends on getting the program bugs squashed, so our schedule has to be as flexible as the sidechains in AutoDock 4.


Lawrence

Hi John.

WCG have licensed the AutoDock code under a different license agreement to the GPL, so I'm afraid there are legal issues with sharing code. However, if you have specific questions, I'm sure the techs will try to help you if they can. I think it would be best if you contacted the techs directly. If you send email to support@worldcommunitygrid.org and mark it for the attention of the FightAIDS project boarding team, you should get the best response possible.

Now that AutoDock has been released under the GPL, WCG will be reexamining the license agreement situation, and hopefully they will be able to release the boarded version of AutoDock eventually. Key word is "eventually", since legal stuff always seems to take forever around here.

And finally, you may be able to get some useful clues just looking at how FightAIDS@Home works. Be aware, however, that there are different versions all named AutoDock 4. The version currently running on WCG is fairly old - from about 2005. The new version in beta (and not working properly yet) is from 2007, but may not be identical to the version released by Scripps as GPL. In particular I noticed your question about command line parameters to boinc_projects. A FAAH work unit looks like this:

<workunit>
    <name>faah1818_d050n997_x2AZ9_01</name>
    <app_name>faah</app_name>
    <version_num>528</version_num>
    <rsc_fpops_est>36369533849631.000000</rsc_fpops_est>
    <rsc_fpops_bound>363695338496310.000000</rsc_fpops_bound>
    <rsc_memory_bound>100000000.000000</rsc_memory_bound>
    <rsc_disk_bound>75000000.000000</rsc_disk_bound>
    <command_line>
-dpf faah1818_d050n997_x2AZ9_01.dpf -gpf d050n997_x2AZ9_01.gpf
    </command_line>
    <file_ref>
        <file_name>faah1818_d050n997_x2AZ9_01_faah1818_d050n997_x2AZ9_01.dpf</file_name>
        <open_name>./faah1818_d050n997_x2AZ9_01.dpf</open_name>
    </file_ref>
    <file_ref>
        <file_name>faah1818_d050n997_x2AZ9_01_AD4_parameters.dat</file_name>
        <open_name>./AD4_parameters.dat</open_name>
    </file_ref>
    <file_ref>
        <file_name>faah1818_d050n997_x2AZ9_01_d050n997_x2AZ9_01.gpf</file_name>
        <open_name>./d050n997_x2AZ9_01.gpf</open_name>
    </file_ref>
    <file_ref>
        <file_name>faah1818_d050n997_x2AZ9_01_d050n997.pdbqt</file_name>
        <open_name>./d050n997.pdbqt</open_name>
    </file_ref>
    <file_ref>
        <file_name>faah1818_d050n997_x2AZ9_01_x2AZ9.pdbqt</file_name>
        <open_name>./x2AZ9.pdbqt</open_name>
    </file_ref>
</workunit>

ups... forget to mention why i thought Autodock 4 is new... because I was always reading things like this:

UPDATE
May 7, 2007

AutoDock 4 is now available for downloading: it is free and available under the GNU General Public License. Click on the "Downloads" tab. And Happy Docking!

... a bit unclear to me... sorry if I am stupid here.