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World Community Grid Forums
Category: Completed Research
Forum: Human Proteome Folding - Phase 2
Thread: Generated protein structures database |
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Thread Status: Active Total posts in this thread: 10
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Where I can look up structures?
Sorry, could not find link. |
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Sekerob
Ace Cruncher Joined: Jul 24, 2005 Post Count: 20043 Status: Offline |
Don't know which of the different subsections are on-line, but found one from the first Human Proteome Folding project: http://biology.plosjournals.org/perlserv/?req...1371/journal.pbio.0050076 which carries a follow through link to http://www.yeastrc.org/pdr/pages/front.jsp It (The YRC PDR) currently contains 9,678,820 descriptions for 5,530,667 proteins from many databases.
----------------------------------------There were many search engine hits with "human proteome folding database" as target.
WCG
----------------------------------------Please help to make the Forums an enjoyable experience for All! [Edit 1 times, last edit by Sekerob at May 4, 2008 8:25:46 PM] |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Don't know which of the different subsections are on-line, but found one from the first Human Proteome Folding project: http://biology.plosjournals.org/perlserv/?req...1371/journal.pbio.0050076 which carries a follow through link to This link is a PLoS article and it talks about yeasts. http://www.yeastrc.org/pdr/pages/front.jsp It (The YRC PDR) currently contains 9,678,820 descriptions for 5,530,667 proteins from many databases. I could not find predicted structure data there. At least for homo sapiens. Are you sure results from WCG was uploaded there? There were many search engine hits with "human proteome folding database" as target. Yes, but I do want to check out one that was created as result of this and HPF1 projects. Is it actually available somewhere for use? |
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Sekerob
Ace Cruncher Joined: Jul 24, 2005 Post Count: 20043 Status: Offline |
Yeast was a topic on which Dr. Bonneau published a paper and was part of HPF(1)! There are many proteins they look at, not only human to see how they fold and what commonalities there exist. SIMAP does a similarity analysis on the same data sets we fold to find the matching parts. In fact many projects use the same and each others data sets to do more/different crunching on them. These expand continuously so some projects run periodic to update their data sets which go back into the pool, eventually.
----------------------------------------Via the Research link at top of this page you can get to e.g. http://homepages.nyu.edu/~rb133/wcg/rbonneau_posts.html and via that came to http://homepages.nyu.edu/~rb133/Struct-pred.html which has the link to Results from the Human Proteome Folding Project can be found at the Public Data Repository associated with the Yeast Resource Center.http://www.yeastrc.org/pdr/pages/front.jsp Would expect for all released parts to be there. All papers from WCG projects are inserted into the 'Publications' post in the Start Here forum. http://www.worldcommunitygrid.org/forums/wcg/viewthread?thread=14467 . Maybe they provide more leads.
WCG
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Following your links I found:
The database is up for yeast and we are working to finish the post-processing for the other 149 genomes (including human). The results will be served via bioNetBuilder (check my lab website in a few weeks) and via a similar web page (again, check the bonneau lab website in a few weeks). Until then we're beta-testing by releasing our results to the yeast community (who are an active community responsible for great numbers of biomedical discoveries). Ok, yeasts are cool. But that won't answer my question. It seems that there is no link to any online database with results of predictions based on human genome. And rest of 147 genomes - but I actually not interested in those. Or, could it be that I still somehow missing the link? SIMAP is a very useful tool. But it have nothing to do with my question. |
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Sekerob
Ace Cruncher Joined: Jul 24, 2005 Post Count: 20043 Status: Offline |
That's fine, at least now you know a bit more and maybe a few other readers too and why yeast was the first hit on my list.
----------------------------------------Good luck in tracking done Human Proteome Structures.... maybe one of the other folding projects like R@H, POEM, F@H have specific Human Proteome databases for public access.... there are zillions: http://www.google.it/search?hl=en&client=...ture+database&spell=1 ttyl
WCG
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Ok, thank you for help.
It just seems very strange, that thousands of you guys working on solving human protein structures for years and it is not published or available anywhere. I mean real 3d structures in PDB format, one that is an outcome of Rosetta software suit, used by WCG client. I was suspecting this, but wasn't sure. And no, R@H is intended to improve structure prediction methods, and F@H trying to study folding trajectories, so both project most of the time use their time solving proteins with already known structure. Never heard of POEM, but anyway, I was interested more in checking out human protein models generated by this project. tyvm |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
As i understood hpf1 +hpf2, the main purpose is (was) to provide researchers with a database of 3d-structures (created by hpf) of human proteins. Reading the posts above, it seems, there is no such database after years of crunching; or am i getting something wrong?
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Sekerob
Ace Cruncher Joined: Jul 24, 2005 Post Count: 20043 Status: Offline |
The yeast db link was provided earlier in this thread. The next link below specifically lists that database:
----------------------------------------http://homepages.nyu.edu/~rb133/software.html Other database references at bottom says "available soon"
WCG
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Thanks for the clarification; and looking forward to the availability of the wcg-results-database.
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