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World Community Grid Forums
Category: Completed Research
Forum: FightAIDS@Home
Thread: Rosetta@Home Designing HIV Vaccines |
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Thread Status: Active Total posts in this thread: 7
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we45dfa35gh3476
Advanced Cruncher Joined: Apr 19, 2006 Post Count: 57 Status: Offline |
http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1177
"Our first vaccine design calculations have just been sent out on rosetta@home! We are taking a number of different approaches to vaccine design; in the calculations that are just being sent out we are aiming to stabilize a portion of the HIV surface protein, GP120, in its active conformation so it can be used as a vaccine. We are keeping the portion of the protein that interacts with a cell surface receptor called CD4 constant, but redesigning the remainder to increase its stability. The lowest energy designs that are returned from all of your runs will be analyzed here, and the most promising of these sent to our collaborators at the NIH for testing as possible vaccines. This first batch of work units is relatively small--look for work units beginning "PSH"; there will be a much larger batch next week and we will give them more informative names so you can tell what you are looking at." |
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depriens
Senior Cruncher The Netherlands Joined: Jul 29, 2005 Post Count: 350 Status: Offline Project Badges: 
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I hope this is an entirely different project than ours, because otherwise we will have an immense loss of computing power when 2 projects try to solve the same issue!
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Sekerob
Ace Cruncher Joined: Jul 24, 2005 Post Count: 20043 Status: Offline |
Dont think ours is looking for vaccine's....last week the scientist said 40 compounds requested from the NCI from pass 1a...i.e. for treatment, rather then prevention......and still no waste, because a vaccine will likely not cover the known 270 variations?
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WCG
----------------------------------------Please help to make the Forums an enjoyable experience for All! [Edit 1 times, last edit by Sekerob at Sep 20, 2006 8:03:17 PM] |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Hi depriens,
I hope this is an entirely different project than ours Baker Lab is working on a HIV vaccine project. FightAIDS@Home is trying to find more protease inhibitors (proteins to bind to the HIV protease molecule). These are completely different approaches. Here is a brief summary of different ways to attack HIV: http://www.aidsmap.com/en/docs/1041B474-49FD-438C-8738-37F59D84E00C.asp Lawrence |
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we45dfa35gh3476
Advanced Cruncher Joined: Apr 19, 2006 Post Count: 57 Status: Offline |
i.e. for treatment, rather then prevention......and still no waste, because a vaccine will likely not cover the known 270 variations? Exactly. While a good vaccine will help prevent new HIV infections (if it works - many trials have tried but no one has succeeded yet - there is still hope)...it will not help the 36.1 million who are already infected with HIV. Our project is trying to find new drugs to help those  (although there are some studies that suggest using protease/reverse transcriptase inhibitors as a preventative measure for high-risk groups [daily doses of certain HIV drugs prevent new HIV infections in HIV- adults].... or a post-exposure measure to prevent new infections [certain drugs, if taken within 72 hours of exposure, prevent HIV infection in like 70-80% of people]) [Edit 4 times, last edit by we45dfa35gh3476 at Sep 20, 2006 9:48:47 PM] |
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depriens
Senior Cruncher The Netherlands Joined: Jul 29, 2005 Post Count: 350 Status: Offline Project Badges:
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That's what I thought, but I wasn't really sure. Good to hear that they're taking a different approach. Thx for the link btw!
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we45dfa35gh3476
Advanced Cruncher Joined: Apr 19, 2006 Post Count: 57 Status: Offline |
More on the actual WU computations, if anyone is interested:
http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1453 We are now using Rosetta@Home to screen our HIV vaccine designs. We are remodeling the protein called GP120, which is responsible for binding with human proteins and initiate the invasion to host cells. The remodeled/redesigned GP120 can potentially be used as a vaccine. (Please see David's journal for more info) The jobs submitted for this will have a prefix "PSH" and future jobs will also carry the name(s) GP120 and OD1 (stands for the outer domain of the GP120) for easy identification. We are using the jobs on Rosetta@Home to refold and refine the sequences came from design runs. We first remodel the backbone using rosetta (~2000+ different backbone conformations), design them to put suitable sequences on for each of the conformations, and then score all these different sequences to find the best ones to test experimentally. The scoring process is very time consuming as each of the 2000+ starting conformations will have to be sampled thoroughly in its local conformational space before we can call definitively which is the best designed sequence. That's when Rosetta@Home comes to the rescue... |
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