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http://srv4.bakerlab.org/rosetta_cgi/cgi
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User of the day
 | Jonathan Jeckell 
I am a regenerated U.S. Army officer with interests in science and technology (particularly physics). I also have a background in strategy and... |
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Server Status
as of 19 Oct 2016 3:00:06 UTC
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| [ Scheduler running ] |
| Total queued jobs: |
7,082,871 |
| In progress: |
261,598 |
| Successes last 24h: |
130,676 |
| Users |
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1,228,355 (+41) |
| Hosts |
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(last day |
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2,158,393 (+131) |
| Credits last 24h |
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22,320,007 |
| Total credits |
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49,398,205,232 |
| TeraFLOPS estimate: |
223.200 |
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Oct 18, 2016
Predictor of the day: Congratulations to quarlington for predicting the lowest energy structure for workunit FFF_256f7e29f7e8886562ef87c8cedf21df_bontchip2016_Wed_Sep_28_21_04_23_PDT_2016_0000712_abinitio_SAVE_ALL_OUT_441320_0 !
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| News | |
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Sep 23, 2016
Some good news!
We recently published an article in Nature titled "Accurate de novo design of hyperstable constrained peptides".
We would like to thank all Rosetta@Home participants for their help with this work.
In the paper, we present computational methods for designing small stapled peptides with exceptional stabilities.
These methods and designed peptides provide a platform for rational design of new peptide-based therapeutics.
Constrained (stapled) peptides combine the stability of conventional small-molecule drugs with the selectivity and potency of antibody therapeutics.
The ability to precisely design these peptides in custom shapes and sizes opens up possibilities for "on-demand" design of peptide-based therapeutics.
Other developments described in the paper:
We can now accurately design 18-47 amino acid peptides that incorporate multiple cross-links.
We can now design peptides that incorporate unnatural amino acids. Specifically, we designed peptides with a mix of natural L-amino amino acids and D-amino acids (mirror images of L-amino acids). D-amino acids tend to provide better protease resistance and lower immunogenicity; both of which are desired properties in a therapeutic peptide. Unnatural amino acids also let us sample much more diverse shapes and functions.
We can now design peptides that are cyclized via a peptide bond between their N- and C-terminus. Cyclic peptides provide increased resistance against exopeptidases as they have no free ends, and thus are ideal candidates for engineering peptide therapeutics.
We are now working to use these computational methods for designing peptides that target therapeutically relevant targets, such as, enzymes that impart antibiotic resistance in pathogenic bacteria.
Structure prediction runs on Rosetta@Home for these designed peptide models played a key role in selection of good designs that were experimentally synthesized and characterized.
Thank you all for your help in making this work possible! -- Gaurav B.
For more information:
IPD News.
Nature paper "Accurate de novo design of hyperstable constrained peptides".
Nature review "The coming of age of de novo protein design".
Sep 12, 2016
In the last few weeks our project has experienced significant issues resulting in slower than usual work unit distribution, result processing, and credit granting. The cause of this was due to the increasingly large number of new hosts causing our database server to become very sluggish and eventually run out of disk space. Our short term solution was to reconfigure and optimize the project configuration and existing database server, purge old data quicker than usual, and temporarily stop resource intense database queries. This recovery mode will continue until the project stabilizes which may take a few days to a week.
An interim solution will be to temporarily upgrade our database server and thanks to our sys admins, we already have a machine ready to go that has plenty of disk space and double the memory. The upgrade will require a day of downtime which is planned to happen early this week.
The long term solution will be a complete system hardware upgrade to all our servers. The BOINC server software will also be upgraded. We are in the process of ordering these machines and hope to have them running within the next few months.
The project is somewhat stable now and clients should be getting work as usual. However, result processing and credit granting may still be slow and our status information/page may not be up to date as we are in recovery mode and our servers continue to catch up on things. Work history will also be shortened to temporarily save space. We expect things to be back to normal in a few days to a week.
Sorry for any inconvenience and thank you for your continued contributions!
Sep 4, 2016
We've had an unplanned project crash. The project is back online but you might experience interruptions while the system catches up.... -KEL [Sun Sep 4 07:53:59 PDT 2016]
Aug 1, 2016
Journal post from David Baker
We all collectively made the cover of the July 22nd Science-check it out! This same issue also has a news feature on our work, and an article on designed icosohedral cages made from two different designed protein building blocks. For more information and links to the papers, see Ratika's post in her thread.
Jul 29, 2016
Another paper from the Baker lab in Science! Designed Protein Containers Push Bioengineering Boundaries.
"In this paper, former Baker lab graduate student Jacob Bale, Ph.D. and collaborators describe the computational design and experimental characterization of ten two-component protein complexes that self-assemble into nanocages with atomic-level accuracy. These nanocages are the largest designed proteins to date with molecular weights of 1.8-2.8 megadaltons and diameters comparable to small viral capsids. The structures have been confirmed by X-ray crystallography. The advantage of a multi-component protein complex is the ability to control assembly by mixing individually prepared subunits. The authors show that in vitro mixing of the designed subunits occurs rapidly and enables controlled packaging of negatively charged GFP by introducing positive charges on the interior surfaces of the two copmonents.
The ability to design, with atomic-level precision, these large protein nanostructures that can encapsulate biologically relevant cargo and that can be genetically modified with various functionalities opens up exciting new opportunities for targeted drug delivery and vaccine design." - from the IPD website.
More information can be found at this link.
Thank you all for your contributions!
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