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Rosetta@Home
2019-07-16: The Audacious Project

As you may have heard, the Institute for Protein Design was recently selected as part of The Audacious Project. This large-scale philanthropic collaboration, which is the successor to the TED Prize, surfaces and funds projects with the potential to change the world.

As a result, we are expanding our Seattle-based team of scientists and engineers who will work together to advance Rosetta, our software for protein design and structure prediction. The funding will also allow us to invest in the equipment, supplies and lab space needed to design and test millions of synthetic proteins.

What challenges will we be tackling? Watch my TED talk to find out.

All of this work ? like everything we do ? will depend on you, the participants in Rosetta@home. Whether it?s creating custom nanomaterials or safer cancer therapies, we rely on the Rosetta@home distributed computing platform. We cannot thank you enough for taking the time to be a part of this exciting research, and we hope you tell at least one friend that they too can play a role in the protein design revolution just by running Rosetta@home.

Thank you,

David Baker
Director, Institute for Protein Design

2019-07-15: Coevolution at the proteome scale

Last week, a report was published in Science describing the identification of hundreds of previously uncharacterized protein?protein interactions in E. coli and the pathogenic bacterium M. tuberculosis. These include both previously unknown protein complexes and previously uncharacterized components of known complexes. This research was led by postdoctoral fellow Qian Cong and included former Baker lab graduate student Sergey Ovchinnikov, now a John Harvard Distinguished Science Fellow at Harvard. Rosetta@home was used for much of the computing required for this work. Congratulations and thank you to all R@h volunteers.

For more information about this work click here.

2019-07-15: Protein arrays on mineral surfaces

Last week, the Baker Lab in collaboration with the De Yoreo lab at PNNL published a report in Nature describing the design of synthetic protein arrays that assemble on the surface of mica, a common and exceptionally smooth crystalline mineral. This work provides a foundation for understanding how protein-crystal interactions can be systematically programmed. Although R@h was not directly used for this research, previously designed subunits were validated using R@h. Congratulations to all R@h volunteers and thank you for your continued contributions.

For more details click here.

2019-06-06: Citizen scientists use Foldit to successfully design synthetic proteins

Citizen scientists can now use Foldit to successfully design synthetic proteins. The initial results of this unique collaboration are described in Nature.

Brian Koepnick, a recent PhD graduate in the Baker lab, led a team that worked on Foldit behind the scenes, introducing new features into the game that they believed would help players home in on better folded structures. Read more from the Baker Lab.

Thanks to all Rosetta@home participants who helped in this study. Many of the designs were validated using forward folding on Rosetta@home.

Read the full manuscript: https://doi.org/10.1038/s41586-019-1274-4 PDF

2019-03-08: IPD's first nanoparticle vaccine

Researchers in the King lab, an affiliate of the Institute for Protein Design, published a report in Cell describing a computer-designed nanoparticle vaccine targeting respiratory syncytial virus (RSV). Although Rosetta@home was not directly used for this study, Rosetta@home volunteers provided computing for related research and development.

From IPD news:

Millions of children will visit hospitals this year, sickened by RSV. Infection is usually mild, causing only fevers, runny noses and frightened parents. But, in severe cases, barking coughs and painful wheezing can indicate serious respiratory complications, including bronchiolitis and pneumonia.

RSV is the primary cause of pneumonia in children under one and is therefore the leading cause of infant mortality worldwide after malaria. Although virtually every child on Earth will get RSV before the age of three, an estimated 99 percent of RSV deaths occur in developing countries. Despite substantial effort, there is not yet a safe and effective vaccine.

Today, an international team of scientists co-led by researchers at the IPD report in Cell a first-of-its-kind vaccine candidate for RSV. It elicits broadly neutralizing antibodies against respiratory syncytial virus in mice and monkeys, paving the way for human clinical trials.

2019-01-14: Another publication in Nature describing the first de novo designed proteins with anti-cancer activity

A report was published in Nature last week describing the first de novo designed proteins with anti-cancer activity.

These compact molecules were designed to stimulate the same receptors as IL-2, a powerful immunotherapeutic drug, while avoiding unwanted off-target receptor interactions. We believe this is just the first of many computer-generated cancer drugs with enhanced specificity and potency.

R@h participants provided computing for forward folding experiments used in this study which helped validate designs. We'd like to congratulate and thank all R@h volunteers who contributed to this work! Thank you!

Read the full article here: https://www.nature.com/articles/s41586-018-0830-7 (PDF)

2019-01-04: Nature article on IPD work voted ?2018 Reader?s Choice?

Readers of Nature?s News & Views selected an article about our work as their 2018 Reader?s Choice!

The article, written by Roberto Chica of University of Ottawa, does a fantastic job detailing our recent publication on de novo fluorescence-activating proteins ? and the challenges of de novo protein design more generally.

2019-01-04: New publication in Nature: programmable heterodimers

A new report was recently published in Nature describing the design of proteins that mimic DNA.

Using computational design, heterodimeric proteins that form double helices with hydrogen-bond mediated specificity were created. When a pool of these new protein zippers gets melted and then allowed to refold, only the proper pairings form. They are all-against-all orthogonal. With these new tools in hand, it may be possible to construct large protein-based machines that self-assemble in predictable ways.

Read the full article here: https://www.nature.com/articles/s41586-018-0802-y (PDF)

We'd like to thank all Rosetta@home volunteers who contributed computing resources used in this work. Thank you!

2018-11-09: De novo design of self-assembling helical protein filaments

Another de novo design publication was released today describing the design of micron scale self-assembling helical filaments based on previously designed repeat proteins for which R@h participants contributed computing towards. Although R@h was not directly used for this study, R@h participants provided computing for related research. Thank you all for your continued contributions.

Read more here in Science.

2018-11-08: De novo design of jellyroll structures

Sorry for the late post. Last week the Baker lab and collaborators published the first example of proteins designed with non-local beta strand topology.

You can read more about this study here and the publication here.

Thanks to all Rosetta@home participants who contributed to this research.

2018-10-31: Discover magazine article about David Baker's progression into the field of protein design

An interesting article was released yesterday in Discover magazine about the historical progression of David Baker's research and how it has evolved into the Rosetta Commons community and the field of protein design. It includes a case example of de novo design research, and a perspective of what novel proteins may enable. Thank you all for your continued help and contributions to this research!

2018-10-02: Rosetta 64 bit linux version 4.08 released

This update includes a fix suggested by rjs5 for the latest linux versions that use glibc 2.27+. Thank you rjs5!

Please post any issues/bugs regarding this app version in this thread.

2018-09-17: Fluorescent proteins designed from scratch

Congrats to all Rosetta@home volunteers who contributed to a recent report in Nature describing the design of a completely artificial fluorescent beta-barrel protein. As described by one of the main authors, Anastassia, in this forum post:

The paper presents many ?firsts? in computational protein design. It is the first de novo design of the beta-barrel fold (one of the most described folds in the past 35 years, yet mysterious until now). It is also the first de novo design of a protein tailored to bind a small-molecule, which requires very high accuracy in the placement of side chains on protein backbones assembled from scratch. Additionally, we could show that these new proteins could fold and function as expected in vivo! We hope that the advances described in the paper will further enable the de novo design of many biosensors and catalysts tailored for specific applications.

Thanks to all the Rosetta@home volunteers who contributed to the validation of our designed proteins and binding sites.

Here is the link to the IPD webpage that contains a copy of the paper. The work was also featured in the news articles below (the news in Science contains a video of one of our proteins glowing in living cells).

https://www.bakerlab.org/index.php/2018/09/12/de-novo-fluorescent-proteins

https://cen.acs.org/physical-chemistry/periodic-table/Designer-protein-tackles-binding/96/i37
http://www.sciencemag.org/news/2018/09/watch-these-new-designer-proteins-light-when-they-hit-their-target

2018-07-03: Congrats to the collaborative WeFold group for their recent paper published in Nature Scientific Reports. Thank you to all R@h volunteers who contributed to this work.

Congrats to the WeFold group for their recent publication, An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12, in Nature Scientific Reports. As CASP13 is currently in full swing, this article describes the results and analysis of the CASP11 and CASP12 WeFold coopetition (cooperation and competition) . Most of the models used by WeFold for CASP12 (and currently for CASP13) were generated by Rosetta@home volunteers. Congrats and Thank you!

2018-04-27: Rosetta Android version 4.10 released

This version uses a relatively recent version of the Rosetta source. It includes updates to the cyclic peptide folding protocol among other code updates and additions since the previous build. Please post comments and issues in this thread.

2018-03-28: Science opinion article about protein engineering and David Baker

Checkout a recent Bloomberg science opinion article about some of the science behind this project, protein engineering, and David Baker, titled Protein Engineering May Be the Future of Science.

2018-02-27: Rosetta 4.07 released

This version contains a bug fix for the cyclic peptide folding protocol. Please post any issues/bugs regarding this application in this thread.

2018-01-04: Charity Event 2018

The Charity Team has chosen Rosetta@home for their 10th annual event to receive extended computation support for 2 weeks (January 14th 2018, 0.01h to January 27th 2018, 23.59h UTC). To participate, BOINC members are asked to leave their ?Home Teams? and join the Charity Team to crunch Rosetta@home together without the normal ?Race Conditions? during this time frame.

To join the Charity Team at Rosetta@home please click here:
https://boinc.bakerlab.org/rosetta/team_display.php?teamid=10787

You can find more information on the Charity Event forums:
http://forum.charity.boinc-af.org/index.php?board=12.0
and about the Charity Team: https://www.seti-germany.de/wiki/Charity_Team

Stats are also available at:
Team Stats (BoincStats): https://boincstats.com/en/stats/14/team/detail/10787/lastDays
User Stats (S

2018-01-02: The New York Times recently published an article about David Baker and Rosetta

Scientists Are Designing Artisanal Proteins for Your Body

The human body makes tens of thousands of cellular proteins, each for a particular task. Now researchers have learned to create custom versions not found in nature....

2017-12-18: Recent Science and Nature publications. Congrats!

Two research publications were released last week in Science and Nature. The Science publication describes work which relied on computations from Rosetta@home most of which were from Android devices. The Nature publication did not directly use Rosetta@home due to the large size of the designs but used Rosetta. Congrats and thank you for your contributions!



Comprehensive computational design of ordered peptide macrocycles. As described in the abstract, macrocyclic peptides composed of l- and d-amino acids were designed by near-exhaustive backbone sampling followed by sequence design and energy landscape calculations. More than 200 designs were predicted to fold into single stable structures, many times more than the number of currently available unbound peptide macrocycle structures. Nuclear magnetic resonance structures of 9 of 12 designed 7- to 10-residue macrocycles, and three 11- to 14-residue bicyclic designs, are close to the computational models. The results provide a nearly complete coverage of the rich space of structures possible for short peptide macrocycles and vastly increase the available starting scaffolds for both rational drug design and library selection methods.

Read more from UW Medicine News.

Evolution of a designed protein assembly encapsulating its own RNA genome. As described in the abstract, synthetic nucleocapsids composed of icosahedral protein assemblies with positively charged inner surfaces were computationally designed. The ability of these nucleocapsids to evolve virus-like properties by generating diversified populations and selecting for improved genome packaging and fitness against nuclease challenge was also explored. The results show that there are simple evolutionary paths through which protein assemblies can acquire virus-like genome packaging and protection. Considerable effort has been directed at ?top-down? modification of viruses to be safe and effective for drug delivery and vaccine applications; the ability to design synthetic nanomaterials computationally and to optimize them through evolution now enables a complementary ?bottom-up? approach with considerable advantages in programmability and control.

2017-12-14: Research of the Year!

Congrats and thank you! Chemical and Engineering News has highlighted our work for research of the year. Your contributions provided much of the computing to make this possible. Thank you!


Read more.

2017-11-21: Our rosetta and android apps have been updated to version 4.06

This app version was built using the latest Rosetta source. Please report issues in this thread.

2017-11-21: Our android app has been updated to version 4.06

This app version was built using the latest Rosetta source. Please report issues in this thread.

2017-10-05: Rosetta@home has contributed to a number of recent publications. Congratulations and thank you!

In Nature: building 20,000 new drug candidates. New de novo designed "mini-protein" binders were custom built to target either a deadly virus or a potent toxin and were shown to afford protection to mice. Read more.



Sensors for the potent opioid fentanyl. Using a fully-automated Rosetta design pipeline, high-affinity fentanyl sensors capable of detecting environmental fentanyl were produced. Read more.



In Science: data-driven protein design. This work achieves the long-standing goal of a tight feedback cycle between computation and experiment and has the potential to transform computational protein design into a data-driven science. Rather than observing thousands of complex natural proteins to try to deduce their folding rules, over 15,000 new, simpler proteins were built ? all designed using Rosetta. Through multiple design rounds, features that led to successful folding were learned and incorporated into the design pipeline. Read more.

2017-10-05: The rosetta application has been updated to 4.04 for Windows platforms

The "rosetta" application has been updated to 4.04 for Windows platforms to address the Windows BOINC client 7.8.2 issues. This is a relatively recent version of the Rosetta software source and will eventually replace the "minirosetta" application. Please report issues/bugs in this thread.

2017-10-03: The minirosetta application has been updated to 3.78

The minirosetta application has been updated to 3.78. This version includes a patch to prevent fatal errors when using the Windows BOINC client version 7.8.2. There are known issues with this client version for Windows platforms and the BOINC developers are working on a fix. To report bugs, go to this thread.

2017-06-23: Welcome to our updated website!

After many years of service, we are happy to announce that our old website and servers have been retired and we have finally released our new website powered by the latest BOINC software and new hardware. Everything is new and modernized.

If you have any comments or would like to report any issues regarding the new website please post your feedback in this thread.

2017-06-21: Project News Jun 21, 2017

We are still transferring data to our new hardware but it should be finished today and the new servers and web site should be online soon. Thanks for your patience.

2017-06-20: Project News Jun 20, 2017

Outage notice. The project will be down for a day or so starting tomorrow as we transition to new servers using the latest BOINC server software.

2017-06-20: Outage notice

Outage notice. The project will be down for a day or so starting tomorrow as we transition to new servers using the latest BOINC server software.

2017-04-03: Project News Apr 3, 2017

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 this thread.

2017-04-03: Our Android application has been updated to version 3.83

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 this thread.

2017-03-10: Project News Mar 10, 2017

We're back! Our domain, bakerlab.org, has been locked by our registrar since Mar 5th - read more about this outage here Technical News.... -KEL [Fri Mar 10 08:02:30 PST 2017]

2017-02-27: Project News Feb 27, 2017

Journal post from David Baker
NOVA recently featured some of the work that all of you are contributing to:
http://www.pbs.org/wgbh/nova/physics/origami-revolution.html (the 8 minute segment on our work starts at 20:30)
The Economist also had an article on the work you are contributing to:
http://www.economist.com/news/science-and-technology/21716603-only-quarter-known-protein-structures-are-human-how-determine-proteins

Your contributions are highlighted particularly clearly in the Geekwire article:
http://www.geekwire.com/2017/big-data-rosetta-protein-puzzles
which is titled "Big data (and volunteers) help scientists solve hundreds of protein puzzles"

2017-01-20: Project News Jan 20, 2017

Journal post from David BakerHi Everybody!
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:
http://www.geekwire.com/2017/big-data-rosetta-protein-puzzles

https://www.theatlantic.com/science/archive/2017/01/unravelling-lifes-origami/513638

http://www.geekwire.com/2017/uw-protein-pockets

thank you again for your invaluable contributions to this research!!
David

2017-01-19: Project News Jan 19, 2017

More good news!
Our paper titled "Protein structure determination using metagenome sequence data" 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!
Here is an interesting perspective written by Johannes Söding about the paper and it's significance, "Big-data approaches to protein structure prediction".
and related news articles:
Big data (and volunteers) help scientists solve hundreds of protein puzzles
Seeking Structure With Metagenome Sequences
Decoding the Origami That Drives All Life

2017-01-09: Project News Jan 9, 2017

Happy New Year! 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
click here. It may take a day or so to get back to normal operation. Sorry for any inconvenience.

2016-09-23: Project News 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".

2016-09-12: Project News 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!

2016-09-04: Project News 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]

2016-08-01: Project News Aug 1, 2016

Journal post from David BakerWe 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.

2016-07-29: Project News 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!

2016-06-17: Project News Jun 17, 2016

A brand new paper from the Baker lab in Nature! 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!
"Design of a hyperstable 60-subunit protein icosahedron" describes the design of a 20-sided nano-sized particle that could be used to deliver drugs or to develop powerful new vaccines.
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.
Paper
Podcast Under 16 June 2016 "Protein football"
Accessible PDF of Nature paper

2016-05-10: Project News May 10, 2016

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'.
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!
The PDF of this article can be found here
https://www.bakerlab.org/wp-content/uploads/2016/05/680.full_.pdf. An
article on this work was also published in Geekwire http://www.geekwire.com/2016/uw-researchers-add-new-twists-protein-designs.

2016-04-28: Project News Apr 28, 2016

We'll be down for an hour or so for some maintenance. Sorry for any inconvenience.

2016-03-31: Project News Mar 31, 2016

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 this thread.

2016-02-12: Project News Feb 12, 2016

Journal post from David BakerThe 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
http://cen.acs.org/articles/94/i6/Designer-Protein-Promising-Antiflu-Agent.html

2016-01-18: Project News Jan 18, 2016

Journal post from David BakerWe 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. Here is the link to the recent Nature paper:
https://www.bakerlab.org/wp-content/uploads/2015/12/Brunette_Nature_2015.pdf

2015-10-12: Project News Oct 12, 2015

The minirosetta application has been updated to 3.65. To report bugs, go to this thread.

2015-09-03: Project News Sep 3, 2015

The minirosetta application has been updated to 3.62. To report bugs, go to this thread.

2015-08-31: Project News Aug 31, 2015

We are experiencing technical difficulties with our servers and are currently troubleshooting. We hope to have things back to normal soon. Sorry for any inconvenience.

2015-06-15: Project News Jun 15, 2015

The minirosetta application has been updated to 3.59. To report bugs, go to this thread.

2015-03-24: Project News Mar 24, 2015

Here is a video of David Baker describing some of the research going on in the lab from his recent talk at the American Association for the Advancement of Science (AAAS) meeting. Note: you may have to scroll down a little to view the video.

2015-03-09: Project News Mar 9, 2015

The minirosetta application has been updated to 3.54. To report bugs, go to this thread.

2015-01-20: Project News Jan 20, 2015

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 this thread.

2015-01-06: Project News Jan 6, 2015

Happy New Year to all! We just posted a brief synopsis of our CASP11 results in this thread post, and would like to say thank you for all your contributions! Thank you all!

2014-08-15: Project News Aug 15, 2014

Here's an update from David Baker on the Institute for Protein Design's progress: Letter from the Director – IPD Update

2014-08-10: Project News Aug 10, 2014

Our servers will be down for a few hours for maintenance. It is taking a bit longer than expected. Sorry for any inconvenience.

2014-08-05: Project News Aug 05, 2014

Slowdown Update: As it turns out, the slow-down experienced during the last week of July was the result of a very large surge in users joining the project through a new campaign by http://charityengine.com. As the servers were behaving properly - just overwhelmed - and DK was on a well-deserved holiday, it was difficult for the rest of us to pin-point the cause. You can see the recent surge here. We are looking at changing/expanding our webserver frontend to be more resilient to surges like this in the future. Yet again, we apologize for the frustration caused. -KEL

2014-07-30: Project News Jul 30, 2014

We are aware of significant network slow-down between the subnet upon which our servers sit and the Internet beyond the UW campus. We are working with the UW's Network Operations team to pinpoint the cause. We apologize for the frustration caused. -KEL

2014-06-20: Project News Jun 20, 2014

Journal post from David BakerWe have recently made great progress in designing self assembling materials from proteins and in designing proteins which selectively kill tumor cells. These efforts have benefited tremendously from Rosetta@Home! News releases on these advances are at
http://hsnewsbeat.uw.edu/story/self-assembling-nanomachines-start-click
http://hsnewsbeat.uw.edu/story/computer-designed-protein-causes-cancer-cells'-death

2014-05-28: Project News May 28, 2014

The minirosetta application has been updated to 3.52. This version includes a couple bug fixes for symmetric modeling. To report bugs, go to this thread.

2014-04-29: Project News Apr 29, 2014

The minirosetta application has been updated to 3.50. For details and to report bugs, go to this thread.

2014-04-02: Project News Apr 2, 2014

Journal post from David BakerThere has been very exciting recent progress in designing vaccines and small molecule binding proteins using Rosetta that is described in two recent papers in Nature. These and other recent advances are described in the new Rosetta@Home Research Updates thread. It was suggested there that we send out a monthly email newsletter describing recent progress--we haven't done this before to avoid clogging everybody's inboxes but we certainly could if there is interest.

2014-02-05: Project News Feb 5, 2014

UPDATE - We successfully moved all the hardware that supports Rosetta@Home to new a home, some 25 m from it's old location. We did this to help balance the heat load in the datacenter as well as gain more physical space and electrical power for future R@H expansion (if we can afford it). -KEL and DOVA

2013-11-10: Project News Nov 10, 2013

Journal post from David BakerAn article mentioning Rosetta@Home recently appeared in the Globe and Mail:
http://www.theglobeandmail.com/news/national/meet-two-pioneers-of-immune-research/article15101089/

2013-10-10: Project News Oct 10, 2013

The minirosetta application has been updated to 3.48. Please report bugs in this thread

2013-09-25: Project News Sep 25, 2013

Journal post from David BakerOur new Institute for Protein Design is making considerable progress as you can see at http://ipd.uw.edu. we are now using Rosetta@home to rigorously evaluate all computer-based designs before we create synthetic genes to make the proteins in the laboratory. this is dramatically increasing our success rate at designing proteins with new functions. your contributions continue to be absolutely invaluable!

2013-05-20: Project News May 20, 2013

Journal post from David BakerWe have discovered how to make several new classes of protein structures! Rosetta@home has been absolutely critical in this work: when we design a sequence to fold into a new structure, the last thing we do before ordering a synthetic gene so we can make the protein in the laboratory is to send it out to you to predict the structure-if it folds to the structure we designed, we go ahead with it, but if you find that the lowest energy state is a different structure we go back to the drawing board. Our success rate in making brand new structures is far higher than I or anybody else ever expected, and the reason the success rate is so high is that your calculations provide a very stringent test of whether the designed sequence will actually fold the way it is supposed to. In the next few weeks I and other scientists here will describe to you the new classes of proteins we are making, and the many applications they will be useful for. Thank you for your absolutely essential contributions to this newly emerging scientific field!

2013-05-17: Project News May 17, 2013

We again experienced networking problems with the backend of the R@H system. We're up and running again, but the system will be sluggish as the backlogged tasks are worked through. -DOVA and KEL [Fri May 17 13:55:23 PDT 2013]

2013-04-26: Project News Apr 26, 2013

The minirosetta application is updated to 3.46. For details and to report bugs, go to this thread

2013-04-24: Project News Apr 24, 2013

The backend network to R@H became 'fussy' over the past week resulting in an overall slowdown in performance (related to the power outage?). The network was 'rebooted' and things are back to normal. -KEL and DOVA

2013-04-12: Project News Apr 12, 2013

The University of Washington and the surrounding neighborhoods expereince a ~2 hour power failure late last night. While the R@H gear is located the UW's datacetner on campus, the equipment is not protected by generator backup. Everything needed to be rebooted and reset up this AM. -KEL and DOVA

2012-09-10: Project News Sep 10, 2012

Journal post from David BakerWe are now testing the latest batch of novel designed proteins that you have helped us create in our brand new Molecular Engineering laboratory at the UW. You can see pictures of the space where the rosetta@home computed designs are being experimentally tested in a recent newspaper article:
http://seattletimes.com/html/localnews/2019068219_molecularlab05m.html

2012-09-04: Project News Sep 4, 2012

Journal post from David BakerA recent paper in Nature Biotechnology describes how we have combined computational protein design with the high throughput DNA sequencing methods developed for sequencing the human genome to generate potent influenza virus inhibitors. These designed proteins block infection by the flu virus in cell culture experiments, and they are now going through the (quite lengthy) process of being developed as possible anti-flu drugs.

2012-08-24: Project News Aug 24, 2012

Rosetta@Home software updated to version 3.41.

2012-06-10: Project News Jun 10, 2012

Journal post from David BakerMany common materials such as silk and wool are made out of regular repeating arrays of proteins, and symmetric protein arrays make up the coats of viruses and many other assemblies inside cells. The ability to robustly design self assembling materials made out of proteins would have huge numbers of applications-the naturally occurring assemblies are useful, but imagine if we could make custom materials for 21st century problems. In this weeks Science magazine, we describe the use of Rosetta to design self assembling protein nano structures with very high accuracy. We are now attempting to create many different types of symmetric materials, and you will be seeing more symmetric calculations on your rosetta@home screen server. Thank you for making possible this completely new approach to nanotechnology!

2012-05-16: Project News May 16, 2012

Rosetta@Home software updated to version 3.31. Addresses issues with improper initialization of inputs in hybrid protocol for comparative modeling.

2012-05-08: Project News May 8, 2012

Journal post from David BakerA big THANK YOU to all of you who have scaled up your contributions to Rosetta@Home-this is a record level of computing power for us and is super well timed. THANKS!!!

2012-04-29: Project News Apr 29, 2012

Journal post from David BakerI have just been told the very good news that Rosetta@home will be the first project of the BOINC pentathlon, and would like to thank all of the participating teams. I also just learned from the discussion thread that Rosetta@home will be the project of the month for BOINC synergy-this is more excellent news!!
Your increased contributions to rosetta@home could not come at a better time! We've been testing our improved structure prediction methodology in a recently started challenge called CAMEO. For most of the targets, the Rosetta@home models are extremely good, but for a minority of targets the predictions are not good at all. We've now tracked down the source of these failures and it is what we are calling "workunit starvation"; in the limited amount of time the Rosetta server has to produce models (2-3 days) in these cases very few models were made-this happens because many targets are being run on the server so that only a fraction of your cpu power is focused on any one target. while we are working to fix this internally, by far the best solution is to have more total CPU throughput so each target gets more models.
You can follow how we are doing at http://www.cameo3d.org/. You will see that Robetta is one of the few servers whose name is not kept secret-this is because Rosetta is a public project. Our server receives targets from CAMEO and soon CASP, sends the required calculations out to your computers through Rosetta@home, and then processes the returned results and submits the lowest energy models.
We are excited that the workunit starvation problem may go away through your increased efforts for Rosetta@home. Thanks!!!

2012-04-27: Project News Apr 27, 2012

Rosetta@Home software updated to version 3.30. Addresses issues with Cartesian Relax and the modeling of disulfides in the hybrid protocol for comparative modeling.

2012-04-08: Project News Apr 8, 2012

Journal post from David BakerI've described in the past our work using Rosetta and Rosetta@Home to create new enzyme catalysts. In Nature Chemical Biology last month we describe the design of an enzyme which destroys organophosphate
nerve agents and pesticides. These compounds kill by blocking key enzymes, and our designed enzyme eliminates this toxicity. This illustrates how Rosetta@Home enzyme design work can help to solve current problems, including man-made problems.

2012-04-05: Project News Apr 5, 2012

Rosetta@Home software updated to version 3.26. This update includes several enhancements for symmetry in the hybrid protocol for comparative modeling. If you encounter any issues, please let us know here

2012-03-30: Project News Mar 30, 2012

Journal post from David BakerIn the last two months we believe we have made quite a breakthrough in structure prediction, and are excited to test the new method in CASP10. We need your help though--we are now testing many aspects of the new approach and are seriously limited by available CPU cycles. There are now so many flu inhibitor design and structure prediction jobs queued up on Rosetta@Home that there is an eight day wait before they are getting sent out to you. This would be a great time to temporarily increase Rosetta@Home's share on your computers and/or recruit new users--we need all the help we can get! thanks! David

2012-03-14: Project News Mar 14, 2012

Rosetta@Home software updated to version 3.24. This update includes support for symmetry in the hybrid protocol for comparative modeling. If you encounter any issues, please let us know here

2012-02-13: Project News Feb 13, 2012

Rosetta@Home software updated to version 3.22.

2012-01-29: Project News Jan 29, 2012

Journal post from David BakerLast year we described in Science magazine the design of a new enzyme which catalyzes a chemical reaction called the Diels Alder reaction involving the formation of two carbon-carbon bonds. This reaction is interesting because no natural enzymes are known to catalyze the reaction. However, it wasn't a very good enzyme, and we asked FoldIt players to try to improve it. As described in Nature Biotechnology this month, remarkably FoldIt players were able to make the designed enzyme 20 times faster by inserting a completely new loop which helps the enzyme bind the chemicals it links together. The combination of Rosetta@Home and FoldIt is turning out to be powerful indeed for solving challenging problems in biomedicine!

2012-01-16: Project News Jan 16, 2012

Journal post from David BakerIn response to requests from many of you, we will be posting descriptions of the many scientific problems currently being tackled with Rosetta@Home on the Science message boards in the next couple of weeks--stay tuned! I also want to describe a new research direction we are now embarking on aimed at future cancer therapies. There are a small set of proteins which are frequently found at much higher levels than normal on the surface of cancer cells. We are starting to design small proteins which bind tightly to these tumor cell markers. If we are successful, we have collaborators who will be testing these proteins for their ability to target cancer cell killing agents to the tumors.

2012-01-13: Project News Jan 13, 2012

Rosetta@Home software updated to version 3.20. This should fix the graphical issues some users were seeing with version 3.19.

2012-01-02: Project News Jan 02, 2012

The hardware hosting the Rosetta@Home project is being moved from one
datacenter to another on the UW campus. We are using this disruption to update the sagging,
aging gear that runs the project. All of this will result in a few days of down time. We
will work to keep the outage to a minimum, but you migh want to grab enough work for a 4-5
day period. We appreciate your patience, interest and continued contributions to our
research. -KEL

2011-12-19: Project News Dec 19, 2011

Rosetta@Home software updated to version 3.19

2011-10-26: Project News Oct 26, 2011

David Baker receives UW Medicine's Inventor of the Year award. From the award announcement " the Inventor of the Year award is given to individuals who have translated research from the bench, through partnerships with the biomedical industry, to a product or process that has had a major impact on healthcare and the local economy" . Read more...

2011-10-22: Project News Oct 22, 2011

Journal post from David BakerToday's issue of Science magazine describes an exciting new approach to HIV vaccine design using Rosetta. In contrast with other viruses such as polio and influenza, inactivated HIV or HIV proteins have not worked as vaccines, and hence as you know there is currently no effective HIV vaccine. Our approach to vaccine design is to take the bits of the HIV surface protein that people make antibodies to, and using Rosetta graft them onto small stable scaffolds that can be made in large quantities and potentially could be useful as vaccines. We've shown earlier that this can be done straightforwardly with Rosetta if the bits of the HIV protein are contiguous along the sequence, but it is much harder if the antibody recognizes multiple bits close in three dimensions but far in sequence. In this paper we show how such "discontinuous" epitipes can be transferred from HIV gp120 to a simple scaffold protein. More work will be required to determine whether this or other vaccine candidates designed using this approach will be effective as HIV vaccines-let us all hope so!!

2011-10-06: Project News Oct 6, 2011

Journal post from David BakerA recent issue of Nature describes an exciting result from Rosetta@home in collaboration with the NMR spectroscopy laboratory of Lewis Kay in Toronto. Like almost all machines, proteins in order to carry out their functions have to move (change their conformation somewhat) but it has been extremely difficult to determine what these conformational changes are. Lewis Kay's group has developed new methods for getting experimental information on the higher energy very shortlived conformations proteins visit while carrying out their functions. This data is not sufficient to determine the structure of these "excited state" conformations using conventional methods. However, as the paper shows, we can use these experimental data to guide Rosetta and Rosetta@home structure calculations, and produce models of these states. We went one step further than this in the paper by using Rosetta design calculations to stabilize the excited state, and subsequent experiments confirmed the validity of the model. This combination of experimental NMR data, Rosetta structure calculations, and Rosetta design should be very powerful in understanding how proteins carry out their functions.

2011-09-19: Project News Sep 19, 2011

Journal post from David BakerToday's issue of Nature Structural Biology reports the determination of the structure of a protein by FoldIt players. This is exciting because it is perhaps the first example of a long standing scientific problem solved by non-scientists. You might read about this in your newspaper; here is a report that does a good job in explaining how FoldIt came out of Rosetta@home:
http://the-scientist.com/2011/09/18/public-solves-protein-structure/

2011-06-18: Project News Jun 18, 2011

Journal post from David BakerThis week's issue of Nature magazine has an exciting article (http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10154.html) describing work we are doing with collaborators using Rosetta to design a new class of inhibitors of amyloid fibril formation. Amyloid fibrils have been implicated in Alzheimer's and many other diseases. The designed peptides are not suitable for use as actual therapeutics in their present form, but hopefully will help lead the way to effective drugs.

2011-06-15: Project News June 15, 2011

The minirosetta application has been updated to version 3.14. For details and to report bugs, go to this thread.

2011-05-18: Project News May 18, 2011

Journal post from David BakerA recent issue of Nature describes an exciting approach we are taking with collaborators to fight Malaria. The title of the paper is "A synthetic homing endonuclease-based gene drive system in the human malaria mosquito" and the PDF is available at my lab web site. The idea is to use enzymes which cut within critical genes in mosquitos to greatly reduce the number of malaria parasite infected mosquitos. There are still many issues that must be overcome for this strategy to be used against malaria in the real world, but this paper is an important first proof of concept of the strategy.

2011-05-14: Project News May 14, 2011

Journal post from David BakerThis week's issue of Science magazine features an article on the use of Rosetta@Home to design novel proteins which bind tightly to the Spanish Flu (H1N1) Influenza Virus. The paper shows that the experimentally determined atomic structure of the complex between one of the designed proteins and the virus is precisely as in the computer model. The designed proteins block the function of the flu surface protein in biochemical tests, and we are guardedly optimistic that the designs will block flu infection. This is an important milestone for computational protein design (and for distributed computing)--the first atomic level accuracy design of a high affinity protein-protein interface, and the designed proteins are exciting leads for new flu therapeutics. In the next few months, we will be using Rosetta@Home to design proteins that bind tightly and hopefully block other pathogens which cause disease. Thanks to all Rosetta@home users for their invaluable contributions to this research!!

2011-05-07: Project News May 7, 2011

Journal post from David BakerGraduate student Shawn Yu is now posting on current Rosetta@home efforts to design inhibitors for viruses that cause disease in the "Design of Protein Interactions" thread on the Science message boards. Take a look if you are interested; he is happy to answer questions in the thread as well.

2011-05-04: Project News May 4, 2011

Journal post from David BakerThe paper on the Rosetta method which allows determination of the structures of a large class of proteins using limited crystallography data has now been published in Nature magazine. Thanks to all of you for making this work possible!

2011-02-23: Project News Feb 23, 2011

Outage Notice: We are going to update our scheduler tomorrow, Thursday the 24th. The project will be offline intermittantly throughout the day.

2011-01-26: Project News Jan 26, 2011

Outage Notice: We will be offline for a brief 1-2 hour period tomorrow, Thursday the 27th, starting at around 10am PST for maintenance.

2011-01-13: Project News Jan 13, 2011

As many of you are probably aware of already, we've been working hard to try to resurrect the project with the resources we have at hand. Today we replaced a very small temporary disk with a larger 3TB one that we received from the vendor a few days ago. With this disk in place we should soon be back up and running. We have yet to restore data from jobs before the disk failure so these older jobs will still be pending. However, all pending jobs will eventually be granted credit. The good news is that the data from the failed disk has been recovered and we are currently copying it to the new disk. Thank you all for your patience.

2011-01-07: Project News Jan 7, 2011

Well, our luck ran out. The SAN controller that has been causing so much trouble in the last few months finally tipped over in a rather distructive fashion, corrupting the binary tree on which the filesystem is based. We're trying to rebuild the thing but the sheer number of files in the filesystem (> 10M files) makes this process very, very slow. We're bringing the project up from a recent backup (12/09/10) but the backup wasn't a perfect replica of the environment, so we're having to scramble to get all the parts working together again. We only need a few more weeks and then our new, next generation SAN will be ready to be put into place... I just thought the old one would last a few more week. I apologize for the hassle and appreciate your patience as we get things online again... KEL 01/07/11

2010-12-10: Project News Dec 10, 2010

Our article on protein energy landscapes done using @BOINC on Rosetta@HOME is out!

2010-12-09: Project News Dec 9, 2010

Today's heros are Keith and Darwin, our systems administrators and hardware architects. Yesterday, our main filesystem crashed hard. There were warning lights flashing behind every disk on the SAN and it looked pretty grim. Thankfully, Keith and Darwin were able to pinpoint the problem to two redundant laser modules for the fiber optic loops (it was amazing and unlucky that both failed). The laser modules have since been replaced and the filesystem is back up. We'll be starting up the project again shortly. Thanks for your patience.

2010-11-23: Project News Nov 23, 2010

Read about recent work using Rosetta to design flu virus inhibitors, HIV vaccines, and HIV destroying nucleases in David Baker's journal and the Design of protein-protein interfaces thread.

2010-11-13: Project News Nov 13, 2010

Our article on protein energy landscapes done using @BOINC on Rosetta@HOME is out!

2010-11-09: Project News Nov 9, 2010

Follow Rosetta@HOME on Twitter! @rosettaathome We will be posting R@H specific scientific updates and interesting research news there!

2010-11-05: Project News Nov 5, 2010

We're back online, thanks!

2010-10-31: Project News Oct 31, 2010

The minirosetta application has been updated to version 2.17. For details and to report bugs, go to this thread.

2010-10-09: Project News Oct 9, 2010

The minirosetta application has been updated to version 2.16. For details and to report bugs, go to this thread.

2010-10-01: Project News Oct 1, 2010

A few days ago our main filesystem went down but we are finally back to normal operation. Sorry for any inconvenience.

2010-09-21: Project News Sep 21, 2010

The minirosetta application has been updated to version 2.15. For details and to report bugs, go to this thread.

2010-09-01: Project News Sept 1, 2010

As many of you have already noticed, we are experiencing some issues with our work unit generators. We are working on a fix right now and will hopefully be back up to speed soon. Thanks for your patience.

2010-08-08: Project News Aug 8, 2010

Rosetta@home related advances have been featured in the national media twice in the last month. The first advance was the design of a protein catalyst that joins two molecules in a way not found in Nature; this was reported in Science magazine in July. The second advance is the finding that FoldIt players can solve hard structure prediction problems; this was reported in Nature magazine this week. These advances were covered in the New York Times, the LA times, and likely in your local newspaper. Thanks to all of you for your contributions to Rosetta@home!

2010-05-18: Project News May 18, 2010

We'd like to thank everyone for the recent dramatic increase in throughput. Our sustained teraflops has been at an all time high and it couldn't have come at a better time with CASP9 in progress and exciting research developments in the lab.

2010-05-10: Project News May 10, 2010

The minirosetta application has been updated to version 2.14. For details and to report bugs, go to this thread.

2010-04-26: Project News Apr 26, 2010

The minirosetta application has been updated to version 2.11. For details and to report bugs, go to this thread.

2010-04-19: Project News Apr 19, 2010

Rosetta@home has been used to design a protein which may neutralize the flu virus. See David Baker's journal for details.

2010-04-12: Project News Apr 12, 2010

The minirosetta application has been updated to version 2.10. For details and to report bugs, go to this thread.

2010-03-10: Project News Mar 10, 2010

We're back! Our domain, bakerlab.org, has been locked by our registrar since Mar 5th - read more about this outage here Technical News.... -KEL [Fri Mar 10 08:02:30 PST 2017]

2010-01-07: Project News Jan 7, 2010

Well, our luck ran out. The SAN controller that has been causing so much trouble in the last few months finally tipped over in a rather distructive fashion, corrupting the binary tree on which the filesystem is based. We're trying to rebuild the thing but the sheer number of files in the filesystem (> 10M files) makes this process very, very slow. We're bringing the project up from a recent backup (12/09/10) but the backup wasn't a perfect replica of the environment, so we're having to scramble to get all the parts working together again. We only need a few more weeks and then our new, next generation SAN will be ready to be put into place... I just thought the old one would last a few more week. I apologize for the hassle and appreciate your patience as we get things online again... KEL 01/07/11

2009-12-23: Project News Dec 23, 2009

The project was shut down temporarily to make modifications to the SAN filesystem. -KEL/DOVA

2009-09-16: Project News Sep 16, 2009

Our filesystem became bogged down late last night. Thanks to Keith, our systems administrator, the project is back online.

2009-09-11: Project News Sep 11, 2009

Based on the current rate of data crunching, the server lag problem should be alleviated through this weekend.

2009-09-10: Project News Sep 10, 2009

The validator and scheduler servers are currently slowly processing a large work unit. We have reprioritized the WU after finding that it is causing server problem. However, it will take a while for the existing jobs to clean out. Meanwhile, server lags are expected.

2009-08-21: Project News Aug 21, 2009

The minirosetta application has been updated to version 1.96 to solve the packaging issue in 1.95. For details and to report bugs, go to this thread.