FightAIDS@Home is the first biomedical distributed computing project ever launched. It is run by the Olson Laboratory at The Scripps Research Institute in La Jolla, California. We provide free software that you download and install. The software uses your computer's idle cycles to assist fundamental research in discovering new drugs, building on our growing knowledge of the structural biology of AIDS. In addition, this research helps us study the mechanisms of multi-drug-resistance that the "super bugs" of HIV use to escape the current anti-AIDS drugs. And this research helps us create, test, refine, and share the tools and protocols that thousands of other labs use in their research against other diseases.
Experiments 143 through 148 target the LEDGF site of HIV integrase. These experiments involve screening 6 libraries (Full NCI, Enamine, ChemBridge, Asinex, Vitas-M and Maybridge). These experiments will help distinguish better sites of among a group of receptor structures even within the same structure. To help read structures in the table below, the "a" and "b" after the 4-character PDB ID designate those receptor structures with alternate residue positions, while the "a" and "b" with the sites (FBP, LEDGF, Y3) designate different sites for the same symmetric structure of HIV IN.
Experiments 139 through 142 are two studies that each target the the combined receptors thus far used for AutoDock Vina. For each study, AutoDock and AD Vina screen either the NCI Diversity Set II* or the Full NCI Set; hence, there are 4 main groupings of virtual screenings. Experiments 139 and 140 will explore the calibration of a receptor when multiple receptors are involved in a virtual screening. Experiments 141 and 142 will investigate the effect of re-orienting the grid box by systematically rotating and translating a protein structure. In these cases, the LEDGF site of the HIV-1 integrase receptor from PDB 3NF8 is used, 1800 versions.
*Note: the current version of the NCI Diversity Set is IV.
Experiments 133 through 138 target the dimer cavity (between the 2 LEDGF sites) of HIV integrase. These experiments involve screening 6 libraries (Full NCI, Enamine, ChemBridge, Asinex, Vitas-M and Maybridge). These experiments will help determine the differences and utility of varying the dimensions of a "docking box."
Experiments 127 through 132 target HIV reverse transcriptase. These experiments involve screening 6 libraries (Full NCI, Enamine, ChemBridge, Asinex, Vitas-M and Maybridge). These experiments will help determine the differences and utility of varying the dimensions of a "docking box."
Experiments 121 through 126 target the active site of HIV protease. These experiments involve screening 6 libraries (Full NCI, Enamine, ChemBridge, Asinex, Vitas-M and Maybridge). These experiments will help determine the differences and utility of varying the dimensions of a "docking box." The focus of these experiments is on the allosteric sites of HIV protease.
FightAIDS@Home, which has been run independently by the Olson Laboratory since 2002, joined the World Community Grid on November 21, 2005. The World Community Grid is a public distributed-computing infrastructure devoted to running projects that will benefit humanity.
In September of 2009, FightAIDS@Home received its 100,000th CPU year fromWorld Community Grid! As of November of 2012, FightAIDS@Home has received over 165,019 CPU years of calculations from World Community Grid!! Thank you all very much for performing these calculations that help us advance the global struggle against HIV/AIDS!!!
World Community Grid is making technology available only to public and not-for-profit organizations to use in humanitarian research that might otherwise not be completed due to the high cost of the computer infrastructure required in the absence of a public grid. IBM Corporation has donated the hardware, software, technical services and expertise to build the infrastructure for World Community Grid and provides free hosting, maintenance and support. We are grateful that the World Community Grid has invited FightAIDS@Home to join their effort.
The FightAIDS@Home client that was inherited from Entropia was not ideal for both the FightAIDS@Home members and the Olson Laboratory. Several features of the Entropia environment were not functional since we took over Entropia's side of the project, and newer versions of the AutoDock code could not be implemented in the system.
Members are informed about their contribution to the project, including the number of job credits they have computed and overall project statistics
3D graphical output shows computational progress
Forums dedicated to the FightAIDS@Home Project allow for discussion and updates
AutoDock and AutoDock Vina is now in an environment to be easily maintained
Linux and Mac OS X-based systems are now supported
WCG has and will continue to help increase awareness of the FightAIDS@Home Project, enabling more advanced computations
To start running FightAIDS@Home on World Community Grid, please go to the updated how to join page, or go directly to the World Community Grid Website.
Note that there is more than one humanitarian project running on the World Community Grid. The default setting for a new member on World Community Grid is to contribute computing power to all of the projects. You may select to contribute only to FightAIDS@Home by editing your profile by going to My Grid on the website for World Community Grid. The My Projects page will allow you to opt-in and out of projects ( by default, you are opted-in to all current projects). For more details information about the process see the how to join page.
Changes to your project selections will take place the next time your computer finishes its current piece of work and returns the result to World Community Grid.
For descriptions of the experiments we perform
on FightAIDS@Home, please check the Status Page.
Results of these FightAIDS@Home experiments, in the form of unprocessed AutoDock dlg files, are available to the public upon request. For further information, e-mail Dr. Daniel N. Santiago: dsantiag ]~[ scripps . edu (replace ]~[ with the @ symbol and remove the spaces). Please include the phrase "FAAH data" in the subject line of your e-mail. Since the amount of data is on the order of many terabytes, you will need to provide suitable media (such as external hard drives) for receiving a copy of these results.
The AutoDock input files ("pdbqt" files) that we generated for several of the ZINC-derived libraries of compounds that we use in the virtual screens on FightAIDS@Home are now available for free at http://zinc.docking.org/pdbqt/.
After achieving some very promising preliminary results, in June, 2011, we submitted a proposal to IBM to create a new project on World Community Grid. To learn more about it, read the Citizen IBM blog post called "I'll Take 'Curing Malaria' for $1,000, Alex". This project, which was launched on World Community Grid's 7th birthday (Nov. 16, 2011), is called the "Global Online Fight Against Malaria" (GO Fight Against Malaria). Would you like to help us fight malaria and HIV/AIDS? If you do want to help, then CLICK HERE to register and join World Community Grid. You can learn more at our new TSRI site for the GO Fight Against Malaria project.
