Instrumented Interconnecteds Intelligent

It’s elementary, my dear Watson. Oh, wait…..I’m not Sherlock Holmes, and a very different Watson is helping me out.

 

And instead of tracking down a clever thief, this Watson helped me start the search for new ways to stop a monster that kills almost a million people each year — most of them children.

The microscopic monster is the pervasive parasite known as Plasmodium falciparum — which causes the deadliest form of malaria and kills more people than any other parasite.  The Watson who is helping me is not a fictional character, or even a real person — it’s IBM’s Watson computing system, which defeated human competitors on the Jeopardy! game show tournament earlier this year.

No, Watson isn’t giving us advice on killing malaria.  Rather, part of the cash prize that Watson won went to Professor Art Olson’s lab at The Scripps Research Institute, where we are using it to create a new project on World Community Grid called the “Global Online Fight Against Malaria,” which launches today.

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It’s the largest computational research project ever performed against drug-resistant malaria.   Unfortunately, many strains of malaria have become resistant to the different drug treatments (they almost always do, eventually).

Working on malaria started as a hobby that I advanced during nights and weekends for a couple years, when I wasn’t working on FightAIDS@Home, Professor Olson’s project on World Community Grid that seeks a cure for HIV.  With persistence and a lot of help from IBM and from fellow Scripps Research scientists, we’re now addressing malaria.

I should emphasize that this initiative seeks new malaria treatments, not a vaccine.  Of course, the two would be complementary; the vaccine will help prevent illness, and drug treatments will address those who never received the vaccine, or for whom the vaccine wasn’t permanently effective.

We will use World Community Grid to computationally evaluate millions of candidate compounds that might disrupt the proteins the Plasmodium parasites need in order to survive, multiply, or infect a person.  If these target molecules can be disabled by the right chemical compounds, then patients infected with superbugs of malaria can potentially be cured.

It’s like trying to find the right key to open a particular lock.  However, both the lock and the keys are flexible — they can change shape, or transform their conformation, as they wiggle, jiggle, dance, expand, and contract in the warm watery environment in which they reside.  In addition to needing to find a complementary match between the different flexible shapes of the lock and the potential keys, both parts of the system also have different charged and partially charged atoms that need to match up well, too.

To make it even trickier, the total number of potential keys that could exist in the universe (the size of “chemical space”) is estimated to be about 10 to the 60th power (yes, that would be a 1 with 60 zeros after it!).   Therefore, we’ll just focus on the types of keys that are somewhat similar to the types of molecules that have already become approved drugs.

Data from the experiments will then be made available to the public.  How cool is that?

What we can accomplish with one year of calculations on World Community Grid could take us over one hundred years to achieve, using the resources we normally have available.  Join the global online family and “GO Fight Against Malaria” with us.

Alex L. Perryman, Ph.D. is a research associate at The Scripps Research Institute.

___________________________________________________________________________

Editor’s Notes:

World Community Grid is fed by spare computing power from the nearly 2 million PCs that have been volunteered so far by 575,000 people in more than 80 countries.  It gives each PC small computing assignments to perform when the devices aren’t otherwise being used by its owners, then sends the results to scientists seeking a faster way to cure disease, find renewable energy materials, create clean water techniques, or develop healthier food staples.

In 2006, 247 million people became infected with malaria — the leading cause of death in Africa for those under age five.  According to the World Health Organization, malaria is both a disease of poverty and a cause of poverty; survivors are often subject to impaired learning, school absences, lost work, and increased economic distress.  Where prevalent, the disease can account for 40 percent of all public health costs.

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32 Comments
 
November 16, 2011
10:07 PM

What will be the link to attach to the project? Right now there’s one Iam using that refers to Malaria Control.net. Its that the same one. Please explain how to attach to yours.

Respectfully;

Jose Zayas, RPh


Posted by: Jose A Zayas Diaz
 
November 17, 2011
6:11 PM

Dear Jose,

The best link to use is:

http://www.worldcommunitygrid.org/research/gfam/overview.do

The Global Online Fight Against Malaria project is not the same project as MalariaControl.net. They are very different (but complementary) types of research. MalariaControl.net studies the epidemiology of malaria (who has it, what strain(s) do they have, where they are, where it’s increasing and decreasing, etc.), while the GO Fight Against Malaria project performs computational structure-based drug discovery calculations in order to find new chemical compounds that can inhibit specific drug targets from the malaria parasite.

Thank you for your interest and your support,
Dr. Alex L. Perryman


Posted by: Alex L. Perryman, Ph.D.
 
November 19, 2011
11:47 AM

Thanks for the man who writed the software algorithm for this project and other man work for this project.I want to know,is there any project about HBV study? or any project about hydrophobia? Can find any algorithm for kill these virus?we know that, there is not effective drug to kill virus in body at present, even influenza virus.Why?can computational algorithm provide any help?


Posted by: liuming
 
December 14, 2011
8:08 PM

Dear liuming,

You’re welcome. And thank you for your interest in our projects.

Two different “docking” programs will be used in the GO Fight Against Malaria project, AutoDock Vina (or “Vina”) and AutoDock 4.2. A whole team of both men and women wrote the AutoDock program. AutoDock4.2’s authors are Garrett M. Morris, Ruth Huey, William E. Hart, William Lindstrom, Alexander Gillet, David S. Goodsell, and Arthur J. Olson. All of these authors were working at The Scripps Research Institute when they created this program, except for William E. Hart, who was at Sandia.

AutoDock Vina’s authors are Oleg Trott and Arthur J. Olson, who were both working at The Scripps Research Institute when they created this program (and who both still work at TSRI).

I am not aware of any World Community Grid projects that are focused on hepatitis B virus or on hydrophobia. To learn more about the different projects that are being performed on World Community Grid, see http://worldcommunitygrid.org

No algorithm is going to kill any actual viruses. But these algorithms can help us discover promising new inhibitors that could possibly be developed into new drugs. To learn more about these types of calculations and how they can help advance drug discovery and development research, see our other project at http://fightaidsathome.scripps.edu (Volume 10 of the FightAIDS@Home Newsletter and the World AIDS Day webinar I gave are both linked at the top of that site, and they will both help answer your question). You can also learn more about the details of this project and of the calculations it utilizes at: http://www.worldcommunitygrid.org/research/gfam/faq.do

There are actually many effective, FDA-approved drugs that can help treat many different kinds of viruses. There are even two drugs that can help stop influenza infections: Tamiflu (also known as Oseltamivir) and Relenza (also known as Zanamivir).

Best wishes,
Dr. Alex L. Perryman


Posted by: Alex L. Perryman, Ph.D.
 
June 22, 2013
6:00 PM

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