原来之前对癌症有突破的foldit程序是Rosetta@home开发的！
本帖最后由 eai 于 2011-10-22 17:51 编辑游戏玩家破解蛋白质谜题，艾滋病、癌症研究有望获重大突破,这一成果刊登在最新的《自然—结构与分子生物学》（Nature Structural & Molecular Biology）杂志上。
http://www.36kr.com/p/48161.html
http://img01.36krcnd.com/wp-content/uploads/2011/09/9mZA1.png
仅用了三周时间，游戏玩家就解决了一个困扰科学家好几年的难题。一群玩家通过玩游戏发现了一种蛋白质的结构，这种蛋白质在艾滋病毒生长过程中起到了至关重要的作用。该发现标志着人类有望在艾滋病毒（HIV）和艾滋病（AIDS）研究领域获得重大突破。这一成果刊登在《自然—结构与分子生物学》（Nature Structural & Molecular Biology）杂志上。
在一款名叫Foldit的游戏中，玩家可以预测逆转录病毒蛋白酶的结构，这种酶在艾滋病毒复制过程中起到了关键作用。从理论上讲，解开这种蛋白质的结构可以帮助科学家开发阻止蛋白酶传布的药物。
“很多人尝试通过分子替代的方法解决M-PMV的晶体结构问题，但都失败了，于是我们向蛋白质折叠游戏Foldit的玩家发起了挑战，让他们制作该蛋白质的精确模型。出人意料的是，这些玩家制作的模型质量很高，可成功地用于分子替代和结构判断。这种更准确的结构为设计抗逆转录病毒药物提供了新的见解。”
人类具有空间推理能力，这是计算机所不擅长的。游戏则提供了一个框架，把计算机和人类的优势整合到一起。Foldit首席设计师Seth Cooper说到。
这项通过Foldit取得的突破不仅可用于艾滋病研究，还可用于癌症和帕金森症的研究。
该研究报告原文：http://www.cs.washington.edu/homes/zoran/NSMBfoldit-2011.pdf
也可在nature看到原文：http://www.nature.com/nsmb/journal/v18/n10/full/nsmb.2119.html
这个foldit软件原来是Rosetta@home项目组做出来的，而且刚刚看了Rosetta@home的网站http://boinc.bakerlab.org/rosetta/，发现最近有很多令人鼓舞的实质性进展，《自然》期刊连续几期都发表Rosetta@home的成果？摘录如下：
1.Oct 6, 2011
Journal post from David Baker
A 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.
2.Sep 19, 2011
Journal post from David Baker
Today'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/
3.Jun 18, 2011
Journal post from David Baker
This 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.
4.
May 18, 2011
Journal post from David Baker
A 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.
看来要多抽一些运算时间出来投入到Rosetta@home项目才行，最新的消息太令人兴奋了， FAH要加把劲才行。 可惜Rosetta@home还没gpu运算，看到分布式运算带来的实质性影响，这两年的付出感觉值得。 本帖最后由 eai 于 2011-10-22 16:24 编辑
Rosetta@home项目看来是走电脑+人脑的研究路线，结合两者的优势来解决蛋白质问题， foldit上面好像也有Team china团队，大家看看自己能否玩得转？看来蛋白质的研发不但要看哪个团队的电脑厉害，还要看哪队的参与者大脑对空间逻辑更聪明 人脑+电脑是个不错的方法，能少浪费不少算力吧 人脑+电脑是个不错的方法，能少浪费不少算力吧
金鹏 发表于 2011-10-22 16:21 http://www.equn.com/forum/images/common/back.gif
最近这个项目出了不少实质成果啊，可能是艾滋和癌症攻克的重大突破，都刊登在《自然》杂志上了 Rosetta@home这个项目也运作了有十年时间吧，看项目的日志，发现比较重大的研究发现都是2010年公布出来的，不容易啊，这就是科学研究！
摘录一下从2010年以来在研发日志上的好消息，不翻译了，看得懂的都应该看看，令人兴奋
1.Message 64989 - Posted 15 Jan 2010
We got some good news today. A manuscript that many of you contributed to through Rosetta@home was just accepted for publication in Science magazine, perhaps the most widely read scientific journal. The paper shows that accurate structures can be calculated using Rosetta for proteins up to 200 amino acids long if even a small amount of experimental data (from NMR experiments) is available to guide the search. This is an exciting advance because it could make it very much faster and easier to experimentally determine protein structures. Thanks everybody for your contributions to this work, and to our ongoing research efforts!
2.Message 65046 - Posted 20 Jan 2010
Sarel has collected many very promising potential flu virus inhibitors from your rosetta@home calculations over the last ten days, and will be selecting a number of them for experimental testing--see his postings in the "design of protein-protein interactions" thread.
3.Message 65483 - Posted 8 Mar 2010
Our paper on solving structures of proteins of up to 200 amino acids using very limited experimental data is in the Feb 19 issue of Science magazine (pg 1014) which is on some news stands now. this wouldn't have been possible without Rosetta@home--thanks again everybody!
4.Message 65709 - Posted 9 Apr 2010
While the results are still preliminary, it appears that Rosetta@home has produced an extremely exciting result! As I described a few posts ago, many of you through rosetta@home contributed to the design of proteins predicted to bind very tightly to the influenza flu virus. We have now completed the first round of testing of the designed proteins, and one of them in the experiments conducted thus far clearly binds very tightly to the virus. Our data also indicate that the binding is at a site critical to the virus invasion of our cells, and so the protein may be able to neutralize the virus. I will keep you posted over the next couple of months as the picture becomes clearer--but for now--thank you all for making this possible!!
5.Message 66165 - Posted 17 May
We are absolutely delighted by the recent increase in the total throughput of rosetta@home, which could not come at a more critical time! we are having to make very difficult choices between CASP9 structure prediction calculations and the next generation of pathogen inhibiting proteins building on our success with the flu virus inhibitor, and the new contributions of computer power many of you are making are helping immensely. Thank you very much!
6.Message 66617 - Posted 21 Jun 2010
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!
7.Message 68287 - Posted 31 Oct 2010
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.
8.Message 69436 - Posted 20 Jan 2011
First, I would like to thank everybody for bearing with us while we recovered from a critical server hardware failure. Over the next month or two we will be installing more powerful and more robust hardware so hopefully this will not happen again.
Second, I'd like to tell you briefly about another exciting success with Rosetta. When structural biologists work to solve protein structures by putting protein crystals into x-ray beams and recording the diffraction pattern, they only have half of the necessary information. The other half (the "phase" information) can be quite difficult to obtain. In the past six months, we've collected about 15 cases where protein crystallographers were stuck and could not solve the structure. Using Rosetta, we built models for these proteins of sufficient quality to allow the inference of the missing information and subsequently the solution of these structures. This opens the door to a much easier way of solving challenging protein structures, and there are lots of scientists excited about using the new method. The new method is described in a manuscript which will likely appear soon in Nature magazine.
Again, thank you for sticking with rosetta@home during our recent server problems -- there is a lot of exciting scientific research that is only possible because of your contributions!
9.Message 70008 - Posted 11 Apr 2011
In a previous post I described the design of small proteins which bind to and block the function of the key surface protein on the influenza virus, called the haemagluttinin (I can never spell that right!). We are very excited about the possibility of making more proteins that bind to the various strains of the virus that could serve as anti flu drugs (this would only be for very acute infections as you probably wouldn't want to take a dose of these too many times) and are actively working on this. Meanwhile, a manuscript describing the design of the first proteins and how they block the haemaglutinin from the Spanish Flu influenza virus has just been accepted as a full research article in Science magazine. We are excited (and nervous) because we've never been this close to making an actual drug before (as I've explained before, most of what we do is directed more at basic understanding than actual drug development). Still, of course, it is a long road (clinical trials, etc if we get that far) to get something to the point it can be used as a drug. I'll keep you posted as we move along with this.
10.Message 70340 - Posted 14 May 2011
This 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!!
(if you want to learn more, the Science web site has a podcast discussing the work:
http://podcasts.aaas.org/science_podcast/SciencePodcast_110513.mp3)
11.Message 70368 - Posted 18 May 2011
A 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.
12.Message 70577 - Posted 18 Jun 2011
This 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.
13.Message 71287 - Posted 19 Sep 2011
Today'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/
14.Message 71385 - Posted 6 Oct 2011
A 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.
Foldit —— 在线蛋白质折叠游戏介绍：
http://www.equn.com/forum/viewthread.php?tid=18296&highlight=foldit 值得高兴 我也去看看 值得高兴 我也去看看 foldit感觉好难玩啊 全英文的有点累 如果有中文的就好了 抽一点打魔兽的时间学一点英文，再玩玩foldit foldit好像是利用了Rosetta@home项目得出的算法和数据构建的，玩家得出来的较好的模型数据由研究机构用实验方法去验证结果，再反馈数据给Rosetta@home项目去改进算法，看了那么多分布式项目，Rosetta@home项目目前好像是做得很不错的一个，对艾滋，癌症，流感的攻克贡献都有目共睹了，虽然这个项目不是直接攻克特定的疾病，但为攻克疾病提供了很多很重要的理论，模型，算法。许多研究疾病的科学家都从这个项目中得到新方法和启发。 为什么今天这么多人讨论foldit呢？
可是我从来没看见过有人讨论过eterna 为什么今天这么多人讨论foldit呢？
可是我从来没看见过有人讨论过eterna
Sharpshooter 发表于 2011-10-23 14:58 http://www.equn.com/forum/images/common/back.gif
主因是近期的《自然》期刊上有一篇关于艾滋研发突破的文章上面提到了 foldit玩家这个名字， 这个研究突破就是基于foldit玩家的游戏结果验证证实出来的。 本帖最后由 eai 于 2011-10-23 15:21 编辑
eterna好像是stanford开发的一套类似foldit的在线游戏吧， FAH版的朋友应该玩一下。
看来foldit在这方面比eterna走得更远一点？
看来只有结合电脑+人脑的优势才能大大加速科研进度，单靠电脑目前来说还是太慢了。目前累积出来的算法和模型还不能让电脑找到解决问题的方法。
我觉得FAH版应该开发一个专题出来讨论eterna这个游戏的
同样RAH版也应该开发一个专题出来专门讨论foldit。
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