Crucial step in AIDS virus maturation simulated for first time
“Bioinformaticians at IMIM (Hospital del Mar Medical Research Institute) and UPF (Pompeu Fabra University) have used molecular simulation techniques to explain a specific step in the maturation of the HIV virions, i.e., how newly formed inert virus particles become infectious, which is essential in understanding how the virus replicates. These results, which have been published in the latest edition of [Proceedings of the National Academy of Sciences, could be crucial to the design of future antiretrovirals.”
HIV proteasa cutting the poly-protein chain. Source: IMIM
Using ACEMD a software for molecular simulations and a technology known as GPUGRID.net, Gianni De Fabritiis’ group has demonstrated that the first ‘scissors proteins’ can cut themselves out from within the middle of these poly-protein chains. They do this by binding one of their connected ends (the N-terminus) to their own active site and then cutting the chemical bond that connects them to the rest of the chain. This is the initial step of the whole HIV maturation process. If the HIV protease can be stopped during the maturation process, it will prevent viral particles, or virions, from reaching maturity and, therefore, from becoming infectious.
This work was performed using GPUGRID.net, a voluntary distributed computing platform [running on BOINC software] that harnesses the processing power of thousands of NVIDIA GPU accelerators from household computers made available by the public for research purposes*. It’s akin to accessing a virtual supercomputer. One of the benefits of GPU acceleration is that it provides computing power that is around 10 times higher than that generated by computers based on CPUs alone. It reduces research costs accordingly by providing a level computational power that previously was only available on dedicated, multi-million dollar supercomputers.”
[*Rest assured, while a small number of projects run on GPU processors, most projects running on BOINC software are CPU based and do not use GPU processing.]
BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience. BOINC is more properly the Berkeley Open Infrastructure for Network Computing, developed at UC Berkeley.
Visit the BOINC web page, click on Choose projects and check out some of the very worthwhile studies you will find. Then click on Download and run BOINC software/ All Versons. Download and install the current software for your 32bit or 64bit system, for Windows, Mac or Linux. When you install BOINC, it will install its screen savers on your system as a default. You can choose to run the various project screen savers or you can turn them off. Once BOINC is installed, in BOINC Manager/Tools, click on “Add project or account manager” to attach to projects. Many BOINC projects are listed there, but not all, and, maybe not the one(s) in which you are interested. You can get the proper URL for attaching to the project at the projects’ web page(s) BOINC will never interfere with any other work on your computer.
MAJOR PROJECTS RUNNING ON BOINC SOFTWARE
SETI@home The search for extraterrestrial intelligence. “SETI (Search for Extraterrestrial Intelligence) is a scientific area whose goal is to detect intelligent life outside Earth. One approach, known as radio SETI, uses radio telescopes to listen for narrow-bandwidth radio signals from space. Such signals are not known to occur naturally, so a detection would provide evidence of extraterrestrial technology.
Radio telescope signals consist primarily of noise (from celestial sources and the receiver’s electronics) and man-made signals such as TV stations, radar, and satellites. Modern radio SETI projects analyze the data digitally. More computing power enables searches to cover greater frequency ranges with more sensitivity. Radio SETI, therefore, has an insatiable appetite for computing power.
Previous radio SETI projects have used special-purpose supercomputers, located at the telescope, to do the bulk of the data analysis. In 1995, David Gedye proposed doing radio SETI using a virtual supercomputer composed of large numbers of Internet-connected computers, and he organized the SETI@home project to explore this idea. SETI@home was originally launched in May 1999.”
SETI@home is the birthplace of BOINC software. Originally, it only ran in a screensaver when the computer on which it was installed was doing no other work. With the powerand memory available today, BOINC can run 24/7 without in any way interfering with other ongoing work.
The famous SET@home screen saver, a beauteous thing to behold.
einstein@home The search for pulsars. “Einstein@Home uses your computer’s idle time to search for weak astrophysical signals from spinning neutron stars (also called pulsars) using data from the LIGO gravitational-wave detectors, the Arecibo radio telescope, and the Fermi gamma-ray satellite. Einstein@Home volunteers have already discovered more than a dozen new neutron stars, and we hope to find many more in the future. Our long-term goal is to make the first direct detections of gravitational-wave emission from spinning neutron stars. Gravitational waves were predicted by Albert Einstein almost a century ago, but have never been directly detected. Such observations would open up a new window on the universe, and usher in a new era in astronomy.”
MilkyWay@Home Milkyway@Home uses the BOINC platform to harness volunteered computing resources, creating a highly accurate three dimensional model of the Milky Way galaxy using data gathered by the Sloan Digital Sky Survey. This project enables research in both astroinformatics and computer science.”
World Community Grid (WCG) World Community Grid is a special case at BOINC. WCG is part of the social initiative of IBM Corporation and the Smarter Planet. WCG has under its umbrella currently eleven disparate projects at globally wide ranging institutions and universities. Most projects relate to biological and medical subject matter. There are also projects for Clean Water and Clean Renewable Energy. WCG projects are treated respectively and respectably on their own at this blog. Watch for news.
Rosetta@home “Rosetta@home needs your help to determine the 3-dimensional shapes of proteins in research that may ultimately lead to finding cures for some major human diseases. By running the Rosetta program on your computer while you don’t need it you will help us speed up and extend our research in ways we couldn’t possibly attempt without your help. You will also be helping our efforts at designing new proteins to fight diseases such as HIV, Malaria, Cancer, and Alzheimer’s….”
GPUGrid.net “GPUGRID.net is a distributed computing infrastructure devoted to biomedical research. Thanks to the contribution of volunteers, GPUGRID scientists can perform molecular simulations to understand the function of proteins in health and disease.” GPUGrid is a special case in that all processor work done by the volunteers is GPU processing. There is no CPU processing, which is the more common processing. Other projects (Einstein, SETI, Milky Way) also feature GPU processing, but they offer CPU processing for those not able to do work on GPU’s.
These projects are just the oldest and most prominent projects. There are many others from which you can choose.
There are currently some 300,000 users with about 480,000 computers working on BOINC projects That is in a world of over one billion computers. We sure could use your help.
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