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World Community Grid Forums
Category: Completed Research
Forum: Human Proteome Folding - Phase 2
Thread: HPF2 Status Update |
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Thread Status: Active Total posts in this thread: 30
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martin64
Senior Cruncher Germany Joined: May 11, 2009 Post Count: 445 Status: Offline Project Badges: 
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On the HPF2 website, I found the Nov-1 '09 Status update, probably published on the website a couple of days ahead of plan...
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
 I was going to wait a couple of days, but you beat me to it! The WCG is celebrating 5 years this November, and we wanted to share some of the successes that we've had with the work you've all been doing.November Update In regards to martin64's question about why we fold the different organisms that we do, I think lawrencehardin's answer hit the nail on the head. Very different organisms share proteins of similar function and fold. As I mentioned in our status update, the WCG grid has allowed us to "cast a wide net." We fold very different proteins from very different organisms in an effort to expand the space of predicted+known protein structures. A biologist might come along, looking for information about a protein in some organism or studying a particular enzymatic process, and find structure predictions for multiple homologs within animals, bacteria, etc. -- Patrick |
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nasher
Veteran Cruncher USA Joined: Dec 2, 2005 Post Count: 1422 Status: Offline Project Badges: 
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always good to have updates from the scientists thank you.
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Thanks! Does this mean there will be updates to the Rosetta code HPF2 uses?
There is significant room for improvement in our methods for selecting native-state conformations from structure predictions and assigning family annotations. With the WCG we've been able to cast a wide net, and now we're interested in the improvement of our algorithms and classifiers. |
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gb009761
Master Cruncher Scotland Joined: Apr 6, 2005 Post Count: 2977 Status: Offline Project Badges: 
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Yes, thanks for the update - they're always appreciated :-)
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
There won't be any changes to the Rosetta code. HPF2, however, performs more Rosetta runs per sequence than HPF1 did. Currently, I'm working on developing folding constraints for Rosetta from evolutionary information. These could be added as additional information to the Rosetta energy function like a prior on certain conformations, but it's doubtful that anything like this would be introduced in the near future.
Improvements would be akin to this paper (one of Dr. Bonneau's earlier Rosetta papers) and involve better recognition of native-state predictions. Improving the performance of rosetta using mu...E.M. Strauss, David Baker Or, an improvement in our protein classification method. Superfamily Assignments for the Yeast Proteom...hard Bonneau, David Baker Rosetta effectively samples a large number of possible folds, but we can better utilize those predictions with stronger algorithms. All of the WCG predictions can be re-analyzed and our database updated if we discover more accurate methods. -- Patrick |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
There won't be any changes to the Rosetta code. HPF2, however, performs more Rosetta runs per sequence than HPF1 did. Currently, I'm working on developing folding constraints for Rosetta from evolutionary information. These could be added as additional information to the Rosetta energy function like a prior on certain conformations, but it's doubtful that anything like this would be introduced in the near future. Improvements would be akin to this paper (one of Dr. Bonneau's earlier Rosetta papers) and involve better recognition of native-state predictions. Improving the performance of rosetta using mu...E.M. Strauss, David Baker Or, an improvement in our protein classification method. Superfamily Assignments for the Yeast Proteom...hard Bonneau, David Baker Rosetta effectively samples a large number of possible folds, but we can better utilize those predictions with stronger algorithms. All of the WCG predictions can be re-analyzed and our database updated if we discover more accurate methods. -- Patrick Very interesting - thank you for the information! |
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Somervillejudson@netscape.net
Veteran Cruncher USA Joined: May 16, 2008 Post Count: 1065 Status: Offline Project Badges: 
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Great that the results can potentially generate more and a better understanding of these proteins
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Somervillejudson@netscape.net
Veteran Cruncher USA Joined: May 16, 2008 Post Count: 1065 Status: Offline Project Badges:
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It seems like very few crunchers are posting, not that i am saying any thing of interest but sure has slowed down. Must be either lost interest or distracted with the fall activities and the economic stuff. I am after Saphire but this project sure generates low point return which I have mentioned before but as after HFCC, HCMD2 and HPF2 Saphire at same time one sees the huge descrepancy, at least with my machines as compaired to the other projects.
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
I think a lot may have given up trying to run it, Rosetta for some reason has trouble with 64 Bit OSes. even tho BOINC runs in 32 bit mode. and works ok with other projects to date.. so this project, I got it dedicated to my olde trusty XP Dual Core box instead of running it on my I7
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