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World Community Grid Forums
Category: Completed Research
Forum: Human Proteome Folding
Thread: CALL FOR QUESTIONS |
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Thread Status: Active Total posts in this thread: 51
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
any more science type questions?
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vepaul
Senior Cruncher Belgium Joined: Nov 17, 2004 Post Count: 261 Status: Offline Project Badges: 
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Hello,
In the 16 september 2005 issue, p.1868 of Science magazine, Philip Bradley et al. (titel : Toward High-Resolution de Novo Prediction for Small Proteins) describe the conformation of some small proteins. Are those proteins also studied on the WCG ? Do the results of the 2 methods fit with each other?  |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
any more science type questions? 1) Some of the proteins in the human proteome are well understood in structure and function, but the majority are not. Approximately what proportion of the ~30,000 proteins are unknown? 2) Amino acids have different charge states at different pH, which may influence folded shape of the amino acid chain. How does the folding simulator take account of this? |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
interesting that you should bring this up. The same high res prediction techniques used by Bradley et al in the recent science article will be used in phase 2 of HPF. So the answer is: yes, once we finish the initial low res scal of genomes with Rosetta in fold prediction mode.
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Hello Dr. Bonneau,
I started reading an abstract of the Sept 16 journal Science issue and I kept coming back to to a statement at the beginning of the abstract which said: "For more than 40 years, people have known the amino acid sequence of a protein specifies its three-dimensional structure, but no one has been able to translate the sequence into an accurate structure, said senior author David Baker, an HHMI researcher at the University of Washington" Would you mind attempting to give an explanation that a layperson can grasp what it means to translate the amino acid sequence into an accurate structure? If people are unable to translate sequence to structure then how do they know that sequence specifies its 3d structure? Thanks, Dan Replogle |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Here is the link ( http://www.worldcommunitygrid.org/forums/wcg/viewthread?thread=2066#11584 ) to an article that starts with "The Protein Structure Initiative (PSI), a national program aimed at determining the three-dimensional shapes of a wide range of proteins, has now determined more than 1,000 different structures." But they are cheating.
 Instead of starting with the amino acid sequence and deriving the 3-D structure [through sheer mental briliance  ], they are actually measuring it in the laboratory.mycrofth |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Hi Dr. Bonneau,
My question about WCG is how many human related genes will the project target. Thanks. |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
My question about WCG is how many human related genes will the project target. This one really deserves a numerical answer, Dr. Bonneau. Whether it is expressed in genes, protein domains, proteins or some combination of the above. The original reason for not giving a fixed numerical target was obvious to everyone who had ever read a proposal from a research project director , but the project has reached a point where the obfuscation can and should be dropped.No rush needed to answer this one if you do not have the figures at your fingertips. Just remember to put a post-it note by your console to research this topic. Also, let us bat any curve balls that get thrown at you. It is easy enough to get mired down in controversies just doing science. There are only 24 hours in a day, and you have a lot to do. Besides, I actually enjoy ..some.. arguing, as long as it is reasonably polite.  mycrofth |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Dr. Bonneau,
----------------------------------------I new to the grid, and I must say that the information you have provided is fantastic. I do have one question..... My sons 8 and 10 yrs have become very intrested in in the project from the explainations I can give them. That being said is there any material you could point me to that would better explain the project to young people. Thank you in advance for your time, Rick [Edit 2 times, last edit by Former Member at Oct 14, 2005 3:22:40 AM] |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
rwillis, If you go to the Research page / Human Proteome Folding page link on our website: http://www.worldcommunitygrid.org/projects_showcase/human_proteome.html
On the bottom of that page is a link to the Institute for Systems Biology. There's some kid-friendly stuff there that is maintained by rbonneau. http://www.systemsbiology.org/Scientists_and_..._Proteome_Folding_Project Hope that helps. |
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