Posts by student

1) Message boards : Rosetta@home Science : Difference between R@h and Folding@home (Message 64017) Posted 11 Nov 2009 by student_ Post: The difference between the the two projects is also covered in the Wikipedia article for Rosetta@home: http://en.wikipedia.org/wiki/Rosetta@home#Comparison_to_similar_distributed_computing_projects.
2) Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (4) (Message 61448) Posted 29 May 2009 by student_ Post: Will the newly designed protein inhibit neuraminidase? For those unfamiliar with neuraminidase, it's one of the two surface proteins in influenza, and represents the 'N' in 'H1N1' -- the technical name for swine flu. (The 'H' is for hemagglutinin.) Also, what are the advantages (and disadvantages) of designing a protein to inhibit the virus's surface protein, rather than designing a simpler molecule? My understanding of mainstream anti-influenza drugs like Tamiflu and Relenza is that they are much smaller and simpler than average proteins. Would it be more difficult to engineer and optimize an expression system like E. coli to manufacture the therapeutic protein than the smaller molecular drug? Could small molecules target the invariant regions of influenza surface proteins that the therapeutic proteins being designed will target?
3) Message boards : Rosetta@home Science : Rosetta@home 'featured article' on Wikipedia (Message 56335) Posted 11 Oct 2008 by student_ Post: After over three months of work and a lengthy review process, Rosetta@home is a now a 'featured article' (FA) on Wikipedia. This represents a first for BOINC projects (and distributed computing projects in general), and should make the article a comprehensive and verifiable source of information to everyone wanting to know more about Rosetta@home. Being FA also implies an opportunity to have the Rosetta@home article appear on Wikipedia's main page as 'Today's featured article'. On that day, on average, a given featured article gets almost 100,000 page views. Appearing there would be great exposure for the project and almost certainly give it at least a temporary boost in computational power. Assuming it doesn't get put there beforehand, the best time to have Rosetta@home appear on Wikipedia's main page would seem to be toward the beginning of CASP9 in summer 2010. Are there any other dates that a temporary boost in TFLOPS would be especially useful?
4) Message boards : Rosetta@home Science : Rosetta/Bakerlabs and the big picture? (Message 56303) Posted 9 Oct 2008 by student_ Post: The Rosetta@home article on Wikipedia gives examples of how the project is involved in disease-related research: see http://en.wikipedia.org/wiki/Rosetta@home#Disease-related_research. For a broader perspective on the project's significance to medical research, see http://en.wikipedia.org/wiki/Rosetta@home#Project_significance.
5) Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (4) (Message 56157) Posted 1 Oct 2008 by student_ Post: Can you make a similar comparison for CASP8 as POEM did here? Data for such comparisons is available through several preliminary CASP8 assessments available here: http://www.reading.ac.uk/bioinf/CASP8/. It would be even more interesting to see some superpositions (like this one of TOP7) of a few high-scoring Rosetta@home structure predictions onto their solved structures (available in the PDB). I described a way to get Rosetta's CASP8 sutrcture predictions here: http://boinc.bakerlab.org/rosetta/forum_thread.php?id=4371&nowrap=true#55719. To superposition proteins in PyMOL, I think the syntax is something like "align nameOfStructure1, nameOfStructure2".
6) Message boards : Number crunching : Daily bandwidth usage for Rosetta@home (Message 56124) Posted 30 Sep 2008 by student_ Post: Let me show you my hosts and what my stats tell me (per month): 684483 min 70MB, max 340MB 684744 min 190MB, max 300MB 715317 min 151MB, max 490MB 836911 min 523MB, max 1049MB Since you're using a proxy, would that reflect the bandwidth that Rosetta@home uses for the average user (who probably is not behind a proxy)? Longer run time = less bandwidth. How does increasing the time a work unit is allowed to run decrease bandwidth usage?
7) Message boards : Number crunching : Daily bandwidth usage for Rosetta@home (Message 56097) Posted 30 Sep 2008 by student_ Post: For an average computer running Rosetta@home all day, what is the typical bandwidth usage in terms of bytes uploaded and downloaded? Is there a way to estimate usage based on number of workunits completed? This is clearly important for users with ISP-set limits on bandwidth usage and has been briefly covered in Rosetta@home forums before, but it seems like a good idea to revisit the topic for any new information.
8) Message boards : Rosetta@home Science : Discussion on Stories from CASP8 (Message 55876) Posted 19 Sep 2008 by student_ Post: I'd be most interested in hearing about the limiting factor affecting the accuracy of protein structure prediction: would it be the Rosetta model itself or the computing power available? Both are limiting factors. With more computing power, the number of decoys increases (thus the chance of finding a very close-to-native structure increases). But computing power isn't everything. There are groups in CASP with fewer average FLOPS that do better than Rosetta depending on the category of prediction (e.g., either comparative or de novo prediction). So Rosetta's methods could always be improved. On a separate note, I've got a few questions about Foldit. Could there be more explanation on how it was it incorporated into CASP8? Are its predictions available for viewing? Is it one of the four servers listed in my previous post? And finally, for anyone interested there are some preliminary CASP8 assessments available here: http://www.reading.ac.uk/bioinf/CASP8/
9) Message boards : Rosetta@home Science : Discussion on Stories from CASP8 (Message 55719) Posted 12 Sep 2008 by student_ Post: The CASP 8 predictions from all participating servers are available at http://predictioncenter.org/download_area/CASP8/server_predictions/. If you're using Windows, the *.tar.gz files there can be unzipped and untarred (i.e., accessed) by using a program like 7-Zip; Mac and Linux users have built in utilities to deal with .tar.gz files. And while you would need to register for an account (also publicly available), the predictions are also more conveniently available at the CASP site by navigating on the left menu to CASP Experiments -> CASP8 (2008) -> Predictions -> Server Predictions. At that page, there are four servers clearly belonging to the Baker group: BAKER-DP_HYBRID, BAKER-GINZU, BAKER-ROBETTA and BAKER-ROSETTADOM. Which of these used Rosetta@home resources? It would also be helpful to know those servers' ID numbers, which I imagine are needed to figure out who made what predictions in the files I linked to.
10) Message boards : Number crunching : Rosetta@Home + GPU... FTW? (Message 55083) Posted 14 Aug 2008 by student_ Post: And as a side question... which is better... R@H or F@H? Rosetta@home seems more diverse than Folding@home. Rosetta@home is involved in protein structure prediction, protein docking, and protein design; Folding@home focuses solely on protein folding. Though I don't know a ton about Folding@home, I don't think they make their services publicly available to the scientific community, unlike Rosetta@home, which essentially tests new methods that get built into Robetta, the Baker lab's free online protein structure prediction service. With Robetta, scientists can get structural information about protein's they're working on.
11) Message boards : Rosetta@home Science : Rosetta@home's work on HIV (Message 55082) Posted 14 Aug 2008 by student_ Post: There's a long chain of messages referring to web sites mentioning HIV at: http://www.worldcommunitygrid.org/forums/wcg/listthreads?forum=101 Thanks Robert. The link above has an extra slash at the end of the URL and didn't work for me; here's a working link: http://www.worldcommunitygrid.org/forums/wcg/listthreads?forum=101. From what I understand, FightAIDS@home doesn't use Rosetta -- they use a different suite of docking and folding methods from the Olson laboratory at the Scripps Research Institute. I'm looking more for an explanation of if/how Rosetta was used in the research mentioned in my opening post -- that is, updates on how Rosetta is/was being used in Stamatatos's research funded by the Gates Foundation, and whether Rosetta was used to get results for the linked presentation.
12) Message boards : Rosetta@home Science : Rosetta@home's work on HIV (Message 55053) Posted 12 Aug 2008 by student_ Post: I've been looking around for scientific papers on HIV research involving Rosetta, but have only been able to find a news article and the summary of an oral presentation (Development of IgG1 b12 scaffolds and HIV-1 env-based outer domain immunogens capable of eliciting and detecting IgG1 b12-like antibodies). Is there any soon-to-be published research on HIV that uses Rosetta? The news article (there are a few similar articles available) is about how Leo Stamatatos was going to use Rosetta@home -- reading elsewhere indicated that it would be for the design of immunogens. Scanning through abstracts on Stamatatos's publications, it doesn't seem like he's published anything in collaboration with the Baker lab. The oral presentation doesn't explicitly mention Rosetta, but it seems safe to assume that RosettaDesign was used in "the design of scaffolds containing the CD4/IgG1 b12 binding loop". Is that so?
13) Message boards : Number crunching : Subpar credit per CPU second for R@H. Why? (Message 54880) Posted 3 Aug 2008 by student_ Post: Rosetta's efficiency has no effect - if you doubled the speed at which Rosetta crunches it wouldn't change the credit assigned, as the basis for the credit assignment would just expect twice as much work for each credit. To change the granted credit, there needs to be a multiplier added to the initial calculation which assigns the decoy-value for each work-unit. I believe that is done on the in-house machines before the jobs are released. The same multiplier would have to be added to the BOINC claimed credit too, otherwise the average claims would drag the decoy's value down, or it could be added to the backerlab's credit-granting calculation, in which case it would have to multiply all of the claimed credit values by the multiplier... Thanks for the clarification. I was going on the assumption that credits approximated FLOPS per the relationship used on the main page (daily credit/100,000 = estimated teraFLOPS), which doesn't seem to reflect the actual situation. How does the multiplier work? Maybe it actually does try to estimate the floating point operations done to produce one decoy for each workunit, or what?
14) Message boards : Number crunching : Subpar credit per CPU second for R@H. Why? (Message 54854) Posted 2 Aug 2008 by student_ Post: According to the BOINCstats project credit comparison, Rosetta@home grants significantly less credit than most other projects for the same amount CPU time. Comparing only the ratio in hosts that work on both projects (e.g. a host the works on Rosetta@home and Einstein@home), the percentage is about 70% compared to Einstein@home, 72% compared to Docking@home, 80% compared to SETI@home, and in general less than average. Optimizing the efficiency of Rosetta@home may not be entirely necessary to increase the network's performance, considering it's almost twice as powerful as it was at the beginning of CASP 7 (37 teraFLOPS then, 70 teraFLOPS now). Since the number of hosts increased less than a third in that two-year time (65,000 then, 85,000 now), Rosetta@home will probably depend on Moore's law more than mass appeal for its growth in CPU power. Is the below average performance basically due to a lack of an optimized application, utilization of 64-bit clients, etc.? In particular with Docking@home, is that project's increased FLOPS/(CPU time) possibly due to it using the CHARMM molecular dynamics package?
15) Message boards : Rosetta@home Science : Publications on R@H's Alzheimer's work? (Message 54643) Posted 25 Jul 2008 by student_ Post: Are there any publications on Rosetta@home's research on Alzheimer's disease (or amyloids in general) per the work mentioned in this thread?
16) Message boards : Rosetta@home Science : Top 7 (Message 54459) Posted 12 Jul 2008 by student_ Post: Thanks! I posted the picture below here.
17) Message boards : Rosetta@home Science : Top 7 (Message 54442) Posted 11 Jul 2008 by student_ Post: I believe this is the one you want here: 1QYS You can display this with any number of viewers available on that website, or you can import the atomic configuration of the model into the tooling of choice. Edit: Or, you could download the game, and open an older puzzle labeled as puzzle 61, and view it, and manipulate it in 3D with the game's controls. ...but, unless you are good with the game :), this is not the native structure of TOP7. 1QYS is the x-ray crystal structure, onto which I'd like to superposition the conformation for TOP7 predicted by Rosetta (like I did for Rosetta's first atomic-level accuracy prediction in CASP here). The reason I'm looking for the predicted atomic coordinates is because it's one of Rosetta's significant accomplishments, and the superposition would be a good feature on the Rosetta@home Wikipedia article I'm working to improve. The Wikipedia administrators are strict about licensing/copyright issues (removing any images without licensing information), so I don't think I would be able to simply crop and upload a picture like the one here, for example, without its creator licensing it under GFDL and/or Creative Commons and letting wiki admins know. If I could create a similar superposition with the predicted and determined coordinates myself, then I would license it as freely available for non-commercial use (which it effectively already is without the license) and add it to the R@H Wikipedia article. Regarding puzzle 61 in FoldIt, I don't imagine it's possible to get the TOP7 structure predicted by Rosetta. If it is, that'd be awesome -- but I'd like to have the graphic accurately reflect the ~1.2 Å RMSD between TOP7's Rosetta-predicted and x-ray crystal structures. Thanks for the pointer though :-)
18) Message boards : Rosetta@home Science : Top 7 (Message 54427) Posted 11 Jul 2008 by student_ Post: I know it's been over a year since this thread began, but I thought this would be a good place to ask another TOP7-related question. Is there a coordinate file for the lowest energy decoy of TOP7 available? Even though graphics showing the superposition of TOP7's best decoy and its crystal structure are available in a lot of places, I'd like to make a visualization of it myself in PyMol if possible.
19) Message boards : Rosetta@home Science : Graphing the gap between known sequences and solved structures (Message 54094) Posted 1 Jul 2008 by student_ Post: Since a large part of the protein structure prediction problem is that structure determination is much slower than sequence discovery, I thought I'd try to graph any data on sequences vs time and structures vs time to visualize that trend. The Protein Data Bank has a nice graph for protein structures vs time. Unfortunately I can't find any similar data for sequences vs time. For sequences data, the NCBI non-redundant protein database seems ideal off the top of my head since it aggregates several different large databases and removes identical sequences. The only way I know how to get the number of sequences in the nr database is to BLAST a protein and look at the report header. Does anyone know an easier way to get that type of high level information from NCBI's databases?
20) Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (3) (Message 52780) Posted 28 Apr 2008 by student_ Post: On the updated "Articles about Rosetta and Rosetta@home" page (http://boinc.bakerlab.org/rosetta/rah_articles.php), the link to "RCSB Protein Data Bank Molecule of the Month: Designer Proteins" (http://www.rcsb.org/pdb/molecules/pdb70_1.html) is dead. Here is a working URL: http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb70_1.html.

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