[BOINC] [生命科学类] Rosetta@home

zyll

看来多搞点比赛还是有好处的 不过CASP9不是Foldit的比赛吗

Youth

CASP是针对整个蛋白质结构预测领域的大赛，不是r@h自家搞的

Youth

http://boinc.bakerlab.org/rosett ... p;nowrap=true#66617

Posted 21 Jun 2010 6:55:51 UTC
Last modified: 21 Jun 2010 6:56:36 UTC

A manuscript describing the results on FoldIt, which many of you contributed to, was just accepted for publication in Nature. The idea for FoldIt came from rosetta@home participants who posted on the message boards about wanting to be able to guide the course of the folding trajectory. Please keep letting us know your thoughts and suggestions!

Rosetta@home has now been directly responsible or closely associated with two papers in Science (one on enzyme design, one on new approaches for structure determination) and two papers in Nature (this one on Foldit, and one last year on endonuclease design for gene therapy) in the last 9 months. This kind of impact at the forefront of scientific research is I think a first for volunteeer computing, and perhaps the strongest indication to date of the power and value of volunteer computing for pushing forward the boundaries of scientific understanding.

Thank you all for your invaluable contributions to our collective efforts!

我们又有一篇论文已经被Nature接收，这篇论文是描述FoldIt项目的研究结果，而FoldIt项目的主意最早就是来自于R@H的志愿者们在留言板上发的帖子，另外，到目前为止，与R@H直接相关的论文已经分别在Science和Nature上发表了两篇，所有这些都是志愿计算对前沿科学研究的重要贡献，感谢所有志愿们无私的奉献~！！！

feynord

牛啊!

feynord

http://boinc.bakerlab.org/rosett ... p;nowrap=true#66957

Message 66957 - Posted 20 Jul 2010 6:20:17 UTC
Last modified: 20 Jul 2010 6:20:49 UTC
The most recent issue of Science magazine has our paper on the use of Rosetta to design a new carbon-carbon bond forming enzyme, along with a commentary. This paper has attracted a lot of attention in the press. Thank you all for your contributions to this work and to our ability to move forward with designing enzymes and other proteins that will hopefully be of use to society in not too long.

最近一期的Science杂志登了我们的一篇文章,关于利用Rosetta来设计一个新的可以催化碳碳键生成的酶.随文章还有一篇评论(译注:杂志社对于他们觉得牛B的文章,会让在相同领域很有影响力同行来写一篇评论介绍).感谢大家的贡献,我们希望早日设计出能够造福社会的新蛋白.

Tynox

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!

cnchina

回复 216# Tynox

译:
    Rosetta@home相关进展上个月两次受国家媒体特别报导。第一项是设计出一种将两个分子结合的蛋白质催化剂，这种方法在自然界中未曾被发现；报导于7月份的《科学》杂志。第二项是发现FoldIt玩家能够解决困难的结构预测问题；报导于这周的《自然》杂志。这些进展同时也被纽约时报、洛杉矶时报等其它本地报纸报导。感谢你们为Rosetta@home所作出的贡献！

Youth

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.

大家也许已经注意到，最近我们的任务生成程序有点问题，我们正在对其进行修复，希望能够尽快恢复正常，感谢大家的耐心。

feynord

Sep 21, 2010
The minirosetta application has been updated to version 2.15. For details and to report bugs, go to this thread.

minirosetta程序更新至2.15. 详细情况和报错请点这里.

feynord

Oct 31, 2010
The minirosetta application has been updated to version 2.17. For details and to report bugs, go to this thread.

minirosetta程序更新至2.17. 详细情况和报错请点这里.

Nov 5, 2010
The project is temporarily down for maintenance. It should be back up in an hour or so. Sorry for any inconvenience.

抱歉,为了进行维护,今天项目会短暂关闭,预计几小时就会恢复.

Nov 5, 2010
We're back online, thanks!

项目恢复了,谢谢!

Nov 9, 2010
Follow Rosetta@HOME on Twitter! @rosettaathome We will be posting R@H specific scientific updates and interesting research news there!

我们加了Twitter! @rosettaathome 我们会刊登R@H的研究进展和新闻!

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.

请阅读最近的David Baker日志,关于蛋白质-蛋白质界面研究的条目,了解设计流感病毒抑制剂,HIV疫苗,以及可杀灭HIV的核酸酶的研究进展.

译注:参见

Message 68287 - Posted 31 Oct 2010 6:08:01 UTC  
There have been exciting developments in our work ...
feynord 发表于 2010-12-13 15:10

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 opticoops (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.

感谢我们的管理员Keith和Darwin,他们修复了于昨日崩溃的主文件系统.项目很快就可以恢复了,给您造成不便请多包涵!

Dec 10, 2010
Our article on protein energy landscapes done using @BOINC on Rosetta@HOME is out!

通过Rosetta@Home,我们发表了一篇关于蛋白质能量图景的研究论文,详情请见这里.

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

最近那个一直困扰我们的主文件系统彻底崩溃了，因此我们需要换个新的。我们的项目后退到了10年12月9日的存盘点。我们对此深表歉意。

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.

我们正在恢复先前崩溃的主文件系统上的数据，我们保证把积分发给所有已经提交的任务，请耐心等待！

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.

明天早10点起会停机维护1-2小时。

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.

明天会停机维护。

May 4, 2011
Journal post from David Baker

The 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!

请阅读最近的David Baker日志。我们在《自然》杂志上发表了一篇论文，介绍了利用Rosetta方法，在仅有有限的晶体结构的不利情况下，确定了一大类蛋白质的结构。感谢你们的帮助让这项研究变为可能！

feynord

http://boinc.bakerlab.org/rosett ... p;nowrap=true#68287

Message 68287 - Posted 31 Oct 2010 6:08:01 UTC  
There have been exciting developments in our work to develop general methods for designing proteins that can bind to and block the activity of any desired target protein. There are now three targets for which we have designed and experimentally validated binders: a widely used "model" protein called lysozyme, a protein involved in biosynthesis in the bacteria that causes tuberculosis, and a key protein on the surface of the H1N1 flu virus. In the flu case, our collaborators have just solved the structure of our designed protein bound to the virus protein and it is amazingly close to our computational design model.

Now that the methods seem to be working pretty well, we are thinking more about applications. One of these is to make cheaper and more robust diagnostics kits. We are now collaborating with groups interested in developing low cost diagnostics for the flu virus (and other pathogens). our designed proteins are very easy to make in large quantities, and our collaborators are going to test how well they work in place of more expensive and less stable antibody molecules in diagnostic kits.

最近我们开发出了设计蛋白质来抑制另一个靶蛋白质的通用方法.用这种方法,我们针对三个靶蛋白质设计了抑制蛋白,并且经过了实验验证.这三个靶蛋白是:溶菌酶,结核杆菌生物合成中的关键蛋白,以及一个H1N1流感病毒的表面蛋白.特别是,我们的合作者解出了我们设计的蛋白结合于流感病毒表面蛋白的复合物结构,不仅证实了设计的蛋白的确能够与病毒表面蛋白相结合,而且这个实验得出的结构与我们的计算机预测惊人的吻合.

我们的合作者将把这种通用方法应用于开发更便宜好用的诊断试剂盒,用于检查流感病毒感染(或者针对其它的病原体).我们设计出的蛋白很容易大规模生产;我们的合作者将测试它们能不能替代现有试剂盒中那又贵又不稳定的抗体蛋白.


http://boinc.bakerlab.org/rosett ... p;nowrap=true#68609

Message 68609 - Posted 13 Nov 2010 21:09:15 UTC
Last modified: 13 Nov 2010 21:13:23 UTC
In the past I've described a brand new approach using Rosetta to design vaccines for which there are not effective current vaccination treatments. HIV, for example, has turned out to be fiendishly effective at evading the immune system, and as you probably know, despite much work there is no really good vaccine. In collaboration with other groups, Rosetta has been used to design small proteins that present "Achilles heel" regions of the virus to the immune system to stimulate the production of antibodies which recognize these regions. The first papers on this have now been published and, while the designed proteins have not yet elicited strongly neutralizing responses, there is considerable excitement over this new approach. You can read about it at
http://www.nature.com/news/2010/100927/full/news.2010.495.html

先前我曾经提到了一种利用Rosetta开发疫苗的方法,特别是针对目前还没有有效疫苗的病原体,比方说完克我们免疫系统的HIV.通过与其他研究组合作,Rosetta设计出了一个小蛋白,它可以将病毒的"阿喀琉斯之踵"递呈给免疫系统,刺激产生能够识别病毒的抗体.关于这个研究的首篇文章已经发表在Nature杂志上.虽然这个小蛋白尚不能导致完全杀灭病毒,但这种新方法很有前途.文章参见
http://www.nature.com/news/2010/100927/full/news.2010.495.html


http://boinc.bakerlab.org/rosett ... p;nowrap=true#68696

Message 68696 - Posted 24 Nov 2010 5:06:21 UTC  
The Gates foundation has just awarded $1,000,000 to a collaborative project to develop specific enzymes that cut within HIV DNA in cells into which the virus has integrated:

http://www.gatesfoundation.org/p ... nounced-101027.aspx

One of the many nasty things about HIV is that it can reside for a long time in a latent state where it can't be detected by the immune system. If we can generate enzymes that cut up the virus when it is hidden inside a genome, its hiding place will be destroyed. Keith Jerome's lab at the UW is developing methods for delivering enzymes to possibly HIV infected cells, and a graduate student working between our groups is using Rosetta to design endonucleases which cut within the HIV DNA sequence. I'll keep you posted on the progress of this exciting project!

比尔和枚琳达盖茨基金会刚刚资助了一百万美元,用于一项合作性研究,开发一种酶,可以切除被感染细胞内艾滋病毒的DNA.详情请见
http://www.gatesfoundation.org/p ... nounced-101027.aspx

HIV病毒的一个NB之处就是它可以长时间潜伏于细胞当中,从而避免被免疫系统发现.如果我们可以设计一种酶,它可以找到被感染细胞基因组内潜藏的HIV基因,然后切除它,HIV就藏不住了.华盛顿大学的Keith Jerome教授负责开发体内输送酶到被感染细胞的方法,而我们联合培养的一个学生将用Rosetta来开发这个核酸内切酶.我会告诉你们任何关于这个项目的进展!