Posts by Admin

1) Message boards : News : Archived news. (Message 111783)
Posted 3 Apr 2017 by Admin
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Our Android application has been updated to version 3.83. This update includes bug fixes and new protocols (specifically for cyclic peptide folding and design), and should be significantly more stable for Android 4 to 7.+ platforms. Please report bugs in <a href=https://boinc.bakerlab.org/rosetta/forum_thread.php?id=6982>this thread</a>.
2) Message boards : News : Archived news. (Message 111782)
Posted 27 Feb 2017 by Admin
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<a name=baker_journal_post_81238></a><b><a href=http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1177&nowrap=true#81238>Journal post</a> from David Baker</b> <br><br>NOVA recently featured some of the work that all of you are contributing to:<br /> <a href=http://www.pbs.org/wgbh/nova/physics/origami-revolution.html>http://www.pbs.org/wgbh/nova/physics/origami-revolution.html</a> (the 8 minute segment on our work starts at 20:30)<br /> <br /> The Economist also had an article on the work you are contributing to:<br /> <a href=http://www.economist.com/news/science-and-technology/21716603-only-quarter-known-protein-structures-are-human-how-determine-proteins> http://www.economist.com/news/science-and-technology/21716603-only-quarter-known-protein-structures-are-human-how-determine-proteins </a> <br /> <br /> Your contributions are highlighted particularly clearly in the Geekwire article:<br /> <a href=http://www.geekwire.com/2017/big-data-rosetta-protein-puzzles>http://www.geekwire.com/2017/big-data-rosetta-protein-puzzles</a> <br /> which is titled &quot;Big data (and volunteers) help scientists solve hundreds of protein puzzles&quot;<br />
3) Message boards : News : Archived news. (Message 111781)
Posted 20 Jan 2017 by Admin
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<a name=baker_journal_post_81066></a><b><a href=http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1177&nowrap=true#81066>Journal post</a> from David Baker</b><br><br>Hi Everybody!<br /> <br /> this has been a good week with papers in this and last weeks Science magazine. your contributions were essential for both breakthroughs! here is some of the press you might find interesting:<br /> <br /> <a href=http://www.geekwire.com/2017/big-data-rosetta-protein-puzzles>http://www.geekwire.com/2017/big-data-rosetta-protein-puzzles</a> <br /> <br /> <a href=https://www.theatlantic.com/science/archive/2017/01/unravelling-lifes-origami/513638>https://www.theatlantic.com/science/archive/2017/01/unravelling-lifes-origami/513638</a> <br /> <br /> <a href=http://www.geekwire.com/2017/uw-protein-pockets>http://www.geekwire.com/2017/uw-protein-pockets</a> <br /> <br /> thank you again for your invaluable contributions to this research!!<br /> <br /> David <br /> <br />
4) Message boards : News : Archived news. (Message 111780)
Posted 19 Jan 2017 by Admin
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More good news! <p> Our paper titled &quot;<a href=http://science.sciencemag.org/content/355/6322/294>Protein structure determination using metagenome sequence data</a>&quot; was released today in the journal Science. We would like to thank all Rosetta@Home participants who provided the computing required for this work. In the paper, we describe using predicted co-evolving contacts from metagenomics sequence data and Rosetta to accurately predict the structures for 622 protein families that are not represented in the PDB. Among these structures, over 100 were new folds. Since experimental protein structure determination is costly and often difficult, this study highlights the ability to use computational methods with metagenomics data for reliably structure determination. With the rapidly growing size of genomics data, the future in mapping the structure space of protein families looks bright! Thank you Rosetta@Home participants! <p> Here is an interesting perspective written by Johannes Söding about the paper and it's significance, &quot;<a href=http://science.sciencemag.org/content/355/6322/248>Big-data approaches to protein structure prediction</a>&quot;. <p>and related news articles: <p> <li><a href=http://www.geekwire.com/2017/big-data-rosetta-protein-puzzles/>Big data (and volunteers) help scientists solve hundreds of protein puzzles</a> <li><a href=http://jgi.doe.gov/seeking-structure-metagenome-sequences/>Seeking Structure With Metagenome Sequences</a> <li><a href=https://www.theatlantic.com/science/archive/2017/01/unravelling-lifes-origami/513638/>Decoding the Origami That Drives All Life</a> <p><img src=https://boinc.bakerlab.org/rosetta/rah/rah_images/Sergey_Science_Jan2017_F3.small.jpg>
5) Message boards : News : Archived news. (Message 111779)
Posted 9 Jan 2017 by Admin
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Happy New Year! <br><br>As many of you are likely aware of, we had an outage yesterday that we are just recently recovering from. The University of Washington campus and surrounding Seattle area had a power outage that lasted for a couple hours. For more info about the outage <a href=http://www.dailyuw.com/news/article_15a99cfa-d613-11e6-a089-f789e4249a1f.html>click here</a>. It may take a day or so to get back to normal operation. Sorry for any inconvenience.
6) Message boards : News : Archived news. (Message 111778)
Posted 23 Sep 2016 by Admin
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Some good news! <p> We recently published an article in Nature titled &quot;Accurate de novo design of hyperstable constrained peptides&quot;. 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 &quot;on-demand&quot; design of peptide-based therapeutics. <p> Other developments described in the paper: <p> <li> We can now accurately design 18-47 amino acid peptides that incorporate multiple cross-links. <li> 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. <li> 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. <p> 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. <p> <b>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.</b> <p>
7) Message boards : News : Archived news. (Message 111777)
Posted 12 Sep 2016 by Admin
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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. <p> 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. <p> 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. <p> 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. <p> Sorry for any inconvenience and thank you for your continued contributions!
8) Message boards : News : Archived news. (Message 111776)
Posted 4 Sep 2016 by Admin
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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]
9) Message boards : News : Archived news. (Message 111775)
Posted 1 Aug 2016 by Admin
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<a name=baker_journal_post_80456></a><b><a href=http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1177&nowrap=true#80456>Journal post</a> from David Baker</b><br><br>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 <a href=http://boinc.bakerlab.org/rosetta/forum_thread.php?id=6377&nowrap=true#80443>Ratika's post in her thread</a>.<br />
10) Message boards : News : Archived news. (Message 111774)
Posted 29 Jul 2016 by Admin
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<b>Another paper from the Baker lab in <i>Science</i>! <a href=http://www.ipd.uw.edu/2016/07/designed-protein-containers-push-bioengineering-boundaries/>Designed Protein Containers Push Bioengineering Boundaries</a></b>. <p> &quot;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. <p> 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.&quot; - from the IPD website. <p> More information can be found at <a href=http://www.ipd.uw.edu/2016/07/designed-protein-containers-push-bioengineering-boundaries>this link</a>. <p>Thank you all for your contributions!
11) Message boards : News : Archived news. (Message 111773)
Posted 17 Jun 2016 by Admin
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<b>A brand new paper from the Baker lab in <i>Nature</i>!</b> Thank you yet again for your contributions, Rosetta@home volunteers. Although R@h was not directly used for these designs due to size and memory limitations, your contributions are instrumental in Rosetta development enabling such science. Thank you! <br /> <br /> &quot;Design of a hyperstable 60-subunit protein icosahedron&quot; describes the design of a 20-sided nano-sized particle that could be used to deliver drugs or to develop powerful new vaccines.<br /> <br /> Author and Baker lab graduate student Yang Hsia spoke on a Nature podcast on the work. Have a listen to hear about this awesome work from the protein design experts themselves! Links below.<br /> <br /> <a href=http://www.nature.com/nature/journal/vaop/ncurrent/full/nature18010.html>Paper</a><br /> <br /> <a href=http://www.nature.com/nature/podcast/index.html>Podcast</a> Under 16 June 2016 &quot;Protein football&quot;<br /> <br> <img src=http://boinc.bakerlab.org/rosetta/rah/rah_images/protein_football_design.png>
12) Message boards : News : Archived news. (Message 111772)
Posted 17 Jun 2016 by Admin
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<a name=baker_journal_post_80192></a><b><a href=http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1177&nowrap=true#80192>Journal post</a> from David Baker</b><br><br>I recommend listening to graduate student Yang Hsia's podcast on designing protein footballs which you can find on the Nature web site this week to go along with his paper. (see Ratika's post for the link if you can't find it). Thank you all again for all of your contributions to our research-we couldn't do it without you!<br />
13) Message boards : News : Archived news. (Message 111771)
Posted 10 May 2016 by Admin
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We've come out with a breakthrough paper in Science titled 'De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity'. <p> This is an exciting and significant breakthrough for de novo protein design. A particular challenge for current protein design methods has been the accurate design of polar binding sites or polar binding interfaces, both of which require hydrogen bonding interactions. Hydrogen bond networks are governed by complex physics and energetic coupling, that until now, could not be computed within the scope of design. The computational method described in this paper, HBNet, now provides a general method to accurately design in hydrogen bond networks. This new capacity should be useful in the design of new enzymes, proteins that bind small molecules, and polar protein interfaces. Thanks Rosetta@home community for your participation and help! <p> An article on this work was also published in Geekwire <a href=http://www.geekwire.com/2016/uw-researchers-add-new-twists-protein-designs>http://www.geekwire.com/2016/uw-researchers-add-new-twists-protein-designs</a>.
14) Message boards : News : Archived news. (Message 111770)
Posted 28 Apr 2016 by Admin
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We'll be down for an hour or so for some maintenance. Sorry for any inconvenience.
15) Message boards : News : Archived news. (Message 111769)
Posted 31 Mar 2016 by Admin
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The minirosetta application has been updated to 3.73. This version includes new protocols and a fix for an improved score function. To report bugs, go to <a href=https://boinc.bakerlab.org/rosetta/forum_thread.php?id=6777>this thread</a>.
16) Message boards : News : Archived news. (Message 111768)
Posted 12 Feb 2016 by Admin
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<a name=baker_journal_post_79521></a><b><a href=http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1177&nowrap=true#79521>Journal post</a> from David Baker</b><br><br>The results on the flu neutralizing protein you helped us design have now been published. You can get the paper, like all of our papers, from our lab web site, and read what journalists are saying at<br />
<br />
http://cen.acs.org/articles/94/i6/Designer-Protein-Promising-Antiflu-Agent.html<br />
17) Message boards : News : Archived news. (Message 111767)
Posted 20 Jan 2015 by Admin
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The minirosetta application has been updated to 3.71. This version includes an improved score function, new protocols, and slightly updated graphics. To report bugs, go to <a href=https://boinc.bakerlab.org/rosetta/forum_thread.php?id=6777>this thread</a>.
18) Message boards : News : Archived news. (Message 111766)
Posted 18 Jan 2016 by Admin
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<a name=baker_journal_post_79421></a><b><a href=http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1177&nowrap=true#79421>Journal post</a> from David Baker</b><br><br>We just published a paper in Nature that depended critically on all of your contributions! You can get the pdf for this paper on our website; you can also get pdfs of the many other papers we've published in the last couple of years that relied heavily on rosetta@home. <br />
19) Message boards : News : Archived news. (Message 111765)
Posted 12 Oct 2015 by Admin
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The minirosetta application has been updated to 3.65. To report bugs, go to <a href=https://boinc.bakerlab.org/rosetta/forum_thread.php?id=6706>this thread</a>.
20) Message boards : News : Archived news. (Message 111764)
Posted 3 Sep 2015 by Admin
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The minirosetta application has been updated to 3.62. To report bugs, go to <a href=https://boinc.bakerlab.org/rosetta/forum_thread.php?id=6706>this thread</a>.


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