Posts by David Baker

1) Message boards : Rosetta@home Science : David Baker's Rosetta@home journal (Message 87961)
Posted 28 Dec 2017 by David Baker
Post:
Yesterday's New York TImes had an overview of the work we are doing with your help:

https://www.nytimes.com/2017/12/26/science/protein-design-david-baker.html

Thank you again for your contributions to science and to our research--we could not do it without you!!
2) Message boards : Rosetta@home Science : David Baker's Rosetta@home journal (Message 81238)
Posted 27 Feb 2017 by David Baker
Post:
NOVA recently featured some of the work that all of you are contributing to:
http://www.pbs.org/wgbh/nova/physics/origami-revolution.html utm_medium=novasocial&utm_campaign=nova_2016&linkId=34331189 (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"
3) Message boards : Rosetta@home Science : David Baker's Rosetta@home journal (Message 81066)
Posted 20 Jan 2017 by David Baker
Post:
Hi 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
4) Message boards : Rosetta@home Science : David Baker's Rosetta@home journal (Message 80456)
Posted 1 Aug 2016 by David Baker
Post:
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.
5) Message boards : Rosetta@home Science : David Baker's Rosetta@home journal (Message 80192)
Posted 17 Jun 2016 by David Baker
Post:
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!
6) Message boards : Rosetta@home Science : David Baker's Rosetta@home journal (Message 79521)
Posted 12 Feb 2016 by David Baker
Post:
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

http://cen.acs.org/articles/94/i6/Designer-Protein-Promising-Antiflu-Agent.html
7) Message boards : Rosetta@home Science : David Baker's Rosetta@home journal (Message 79421)
Posted 18 Jan 2016 by David Baker
Post:
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. Here is the link to the recent Nature paper:

https://www.bakerlab.org/wp-content/uploads/2015/12/Brunette_Nature_2015.pdf
8) Message boards : Rosetta@home Science : New "Nature" article by Dr. Baker and co-authors (Message 79420)
Posted 18 Jan 2016 by David Baker
Post:
Yes-Rosetta@home was essential for the design of novel proteins described in the Nature paper "Exploring the repeat protein universe using computational protein design". You can get the PDF from our website as usual. We wrote the beginning and end of the paper to be accessible to a broad audience so please do take a look! Thank you again for critical contributions to this project and all of the current work in the group!
9) Message boards : Rosetta@home Science : David Baker's Rosetta@home journal (Message 76855)
Posted 20 Jun 2014 by David Baker
Post:
We 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%E2%80%99-death
10) Message boards : Rosetta@home Science : Rosetta@home Research Updates (Message 76622)
Posted 15 Apr 2014 by David Baker
Post:
They are gearing up to test MB17 in real cancer cells so we'll keep our fingers crossed. We'll keep you updated as new developments arise.


Any updates if the MB17 worked on the cancer cells? I can not seem to get an answer to this?

Tom Zolotor



experiments are still underway in our collaborators lab at St. Judes hospital
11) Message boards : Rosetta@home Science : David Baker's Rosetta@home journal (Message 76576)
Posted 2 Apr 2014 by David Baker
Post:
There 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.
12) Message boards : Rosetta@home Science : David Baker's Rosetta@home journal (Message 76180)
Posted 10 Nov 2013 by David Baker
Post:
An article mentioning Rosetta@Home recently appeared in the Globe and Mail:

http://www.theglobeandmail.com/news/national/meet-two-pioneers-of-immune-research/article15101089/
13) Message boards : Rosetta@home Science : David Baker's Rosetta@home journal (Message 76065)
Posted 25 Sep 2013 by David Baker
Post:
Our new Institute for Protein Design is making considerable progress as you can see at http://depts.washington.edu/ipd/. 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!
14) Message boards : Rosetta@home Science : David Baker's Rosetta@home journal (Message 75630)
Posted 20 May 2013 by David Baker
Post:
We 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!
15) Message boards : Rosetta@home Science : DISCUSSION of Rosetta Insight (Message 75629)
Posted 20 May 2013 by David Baker
Post:
sorry-things have been very busy here! lots of exciting stuff happening-happy to discuss/answer questions, etc.
16) Message boards : Rosetta@home Science : David Baker's Rosetta@home journal (Message 75215)
Posted 11 Mar 2013 by David Baker
Post:
We have learned to design a new class of proteins which could be useful both as drugs and in sensors. As I've explained before, most drugs are small molecules with fewer than 50 atoms. There are many drugs, such as blood thinning agents, which are very dangerous if given in too large doses. We have succeeded in designing proteins which bind to specific small molecules very tightly. These proteins could be used as antidotes in case of overdose with the target small molecule-for example we've designed a protein which could be useful to treat toxicity due to overdose of the drug digoxin used to treat heart disease. With collaborators, we are working to use these designed proteins to detect levels of the target small molecules in the blood or in the environment.
17) Message boards : Rosetta@home Science : CASP 10 (Message 74991)
Posted 27 Jan 2013 by David Baker
Post:
Was there a general sense after the CASP 10 results came out that the state of the art in protein folding is advancing? Because looking at the overall TM_1 and GDT_1 scores and other metrics for the highest-ranking groups in CASP 10 there doesn't seem to be any improvement over the results from previous competitions: in fact they were slightly worse. A different set of proteins certainly but still wouldn't some incremental improvements be expected?


Yes, there was definitely progress. Since most of the predictions used structures of homologues as starting points, you have to look at the improvements of the predictions relative to these starting models. we are just putting together a paper on this, and I'll post the results when we have everything together.
18) Message boards : Rosetta@home Science : CASP 10 (Message 74803)
Posted 29 Dec 2012 by David Baker
Post:
Is there any point in running the work named "rb" now?
Since we are past August, that was put up as deadline in the first post.


yes! we are now trying to improve Rosetta using the CASP proteins as test cases now that we know the correct solutions.
19) Message boards : Rosetta@home Science : David Baker's Rosetta@home journal (Message 74738)
Posted 15 Dec 2012 by David Baker
Post:
The CASP10 meeting just finished and all the results are on line so you can see what all your contributions made possible! Ray has posted a great summary of the results in the CASP10 thread on the science message boards. Overall, Rosetta@home was top or near top in most categories. I hate to embarrass David Kim who created RosettaHome and has kept it going, but his contact guided predictions were the highlight of CASP10 as they were vastly better than those of any other group. You can see this at
http://predictioncenter.org/casp10/results.cgi?view=targets&model=all&tr_type=others&groups_id=4
David's predictions are the black lines, those of other groups are in orange, better models stay below the rest of the pack.

Thanks to all of you who contributed to CASP10!!
20) Message boards : Rosetta@home Science : David Baker's Rosetta@home journal (Message 74231)
Posted 10 Nov 2012 by David Baker
Post:
We would like to acknowledge the Rosetta@Home participants who found the lowest energy structures for Nobu and Rie's designed proteins:

Fold-I : Aalelan (United States)
Fold-II : Jef (United States)
Fold-III : georgebg (Bulgaria)
Fold-IV: medvjet009(Czech Republic)
Fold-V : _2e_ Russia.

See Nobu's message board thread on "Principles for designing ideal protein structures" (http://boinc.bakerlab.org/rosetta/forum_thread.php?id=6113) for more information including a figure illustrating the critical role played by Rosetta@home in this work. And check out the latest on slashdot:
http://science.slashdot.org/story/12/11/09/020241/proteins-made-to-order
This and other publications from the lab are available at depts.washington.edu/bakerpg

Thanks again to everybody!!


Next 20



©2020 University of Washington
http://www.bakerlab.org