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[BOINC] [生命科学类] Rosetta@home

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发表于 2011-5-18 21:56:11 | 显示全部楼层
2011年5月18日

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.

翻译(by feynord):
最近一期的《自然》杂志刊登了一篇文章,为我们描述了一种抗击疟疾的新途径。文章的题目是"通过人工合成的内切酶来基因改造传播疟疾的蚊子"。通过这种内切酶来切除蚊子的关键基因,将使能够传播疟原虫的蚊子数量大大降低。虽然这项技术离实际应用还有一定距离,但这篇文章至少证明了这种策略可行。


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发表于 2011-10-28 10:23:04 | 显示全部楼层
2011-10-26: Rosetta@Home - Project News Oct 26, 2011
Rosetta@Home software updated to version 3.17

2011-10-26: Rosetta@Home - 项目新闻 Oct 26, 2011
Rosetta@home 软件更新到版本3.17

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发表于 2012-12-8 00:16:27 | 显示全部楼层
貌似跟F@H有点异曲同工之妙 学习了
发表于 2013-5-22 08:03:45 | 显示全部楼层
2013.5.20
David Baker的Journal post:我们发现了几种全新蛋白质结构的合成方法。Rosetta@home在这之中做了十分突出的贡献:在设计用于折叠成新蛋白质结构氨基酸序列时,我们的最后一项工作就是将这个序列发送到各位志愿者的计算机来预测它是否会折叠成我们设计的结构。是的话,我们就开始在实验室合成。否则,如果您发现这个序列处于最低能量状态时是别的结构,那么我们就会回到设计阶段。我们做出全新结构蛋白质的成功率远高于我或其他任何人所期待的。而我们成功率如此高的主要原因,就是您们计算机的运算提供了一个十分严格的测试,即验证我们所设计的(氨基酸)序列是否会如我们所设想的那样折叠。接下来的几周里,我与项目的另外几位科学家会给各位详细描述这几种新类型的蛋白质,并介绍它们在各领域的应用前景。感谢各位在这个新兴科学领域中做出的不可或缺的重要贡献!

完毕,译文比较粗糙见谅。。


2013-05-20: Rosetta@Home, 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!

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发表于 2013-9-2 14:23:01 | 显示全部楼层
本帖最后由 feynord 于 2013-9-3 13:28 编辑

占楼备用

Message 74738 - Posted 15 Dec 2012 14:31:41 UTC
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/casp ... =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!!

2012年12月15日CASP10大赛顺利落幕,所有的结果都在网上公布了,大家可以去看自己的贡献了!参见Ray的总结帖。Rosetta@home在几乎所有的项目中都表现优异。在此我要感谢David Kim,他创立并维护着Rosetta@home,在CASP10中预测之准确超过其他所有的研究组。参见这个网页,David的预测是(每个蛋白质右侧小图中的)黑线,其他研究组的结果是桔黄色线,线越低越好哦。
感谢志愿者们为CASP10做出贡献!

Message 75215 - Posted 11 Mar 2013 1:31:45 UTC
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.

2013年3月11日
我们学会了该如何去设计一类既可能当药物也可能用于检测的蛋白质。要知道很多药物如果用药过量后果就会很严重,比方说抗血栓药物,而多数药物都是小分子药物,分子本身最多包含50个原子。最近我们就成功设计了一些可以紧密结合小分子的蛋白质。一旦用药过量,这些蛋白质也许可以当做解药。比方说,我们最近设计了一个蛋白质,可以用于心脏病药物地高辛的过量解毒。我们正在与其他的实验室合作,用这些蛋白质来检测血液样本或环境中的小分子药物。

Message 75630 - Posted 20 May 2013 6:00:18 UTC
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!

2013年5月20日
参见http://www.equn.com/forum/forum. ... d=501655&ptid=25064





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发表于 2013-11-10 22:45:47 | 显示全部楼层
2013-11-10: Rosetta@Home, 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/

David BakerAnd 涉及到 Rosetta@Home 的日志文章最近发表在加拿大《环球邮报》上:http://www.theglobeandmail.com/news/national/meet-two-pioneers-of-immune-research/article15101089/

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辛苦啦~~: 5.0
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对应翻译贴:http://www.equn.com/forum/thread-38781-1-1.html  发表于 2013-11-14 09:26

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发表于 2014-2-7 17:04:44 | 显示全部楼层
2014.1.5
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 & DOVA

启用了一个新机房

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发表于 2014-5-9 10:18:03 | 显示全部楼层
2014.4.29
Apr 29, 2014
The minirosetta application has been updated to 3.50. For details and to report bugs, go to this thread.

minirosetta计算程序升级至3.50版

2014.4.2
Apr 2, 2014
Journal post from David Baker

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.

Rosetta@Home在Nature上新发表了两篇论文
发表于 2015-1-11 21:57:27 | 显示全部楼层
2015-01-06: Rosetta@Home, 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!大家新年好!我们刚刚在此贴内发布了关于CASP11计算结果的简要摘要。十分感谢您给予我们的帮助!谢谢大家!

http://boinc.bakerlab.org/rosetta/forum_thread.php?id=6574&nowrap=true#77808
发表于 2017-3-6 22:49:35 | 显示全部楼层
2017-02-27: Rosetta@Home, 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/sc ... -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"

大意:NOVA最近发布了有关于Rosetta@home项目的纪录片,在线观看(第十八分钟开始)https://www.bilibili.com/video/av8901529/ ,经济学人杂质也刊登了相关信息。

发表于 2017-12-6 00:32:12 | 显示全部楼层
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.



Rosetta最近又在若干期刊上发表了多项研究成果,感谢您对项目的贡献!

2017.10.05
Massively parallel de novo protein design for targeted therapeutics (https://www.nature.com/articles/nature23912
官网报道:New article in Nature: building 20,000 new drug candidates (https://www.bakerlab.org/index.php/2017/09/28/new-article-nature-designing-testing-20000-new-protein-drug-candidates/

2017.09.19
Computational design of environmental sensors for the potent opioid fentanyl (https://elifesciences.org/articles/28909
官网报道:Sensors for the potent opioid fentanyl (https://www.bakerlab.org/index.php/2017/09/25/sensors-potent-opioid-fentanyl/

2017.07.14
Global analysis of protein folding using massively parallel design, synthesis, and testing(http://science.sciencemag.org/content/357/6347/168
官网报道:New article in Science: data-driven protein design(https://www.bakerlab.org/index.php/2017/08/27/data-driven-protein-design/

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给力哟!: 5.0
给力哟!: 5
  发表于 2017-12-6 11:32

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发表于 2017-12-6 20:51:33 | 显示全部楼层
三篇文章的标题:
大规模并行运算下的新蛋白质设计于靶向治疗
强效阿片类药物芬太尼环境传感器的计算机设计
使用大规模并行设计,合成和测试的蛋白质折叠之全局分析

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发表于 2017-12-15 09:16:18 | 显示全部楼层
2017-12-14: Rosetta@Home, 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!


https://boinc.bakerlab.org/rosetta/forum_thread.php?id=12348


-------------------------
2017.12.14 Rosetta@Home被评为年度重要研究

恭喜各位!同时也感谢各位!化学与工程新闻周刊(Chemical and Engineering News ,美国化学学会出版的周刊)授予了Rosetta@Home “年度研究”的称号。多亏了各位贡献的巨大算力,才是我们能够获得如此殊荣。谢谢!





发表于 2017-12-19 14:41:23 | 显示全部楼层
2017-12-18: Rosetta@Home, Recent Science and Nature publications. Congrats!

祝贺 Rosetta@home 最近在《自然》和《科学》杂志上发布论文!

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!

《科学》杂志上的论文所依赖的计算机算力均来自于 Rosetta@home~(其他 大部分还是安卓设备)
《自然》杂志虽无直接提到 Rosetta 但是确使用到了项目的算力。祝贺并感谢大家的贡献呢~

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.


项目新闻:https://boinc.bakerlab.org/rosetta/forum_thread.php?id=12357

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发表于 2018-1-3 13:57:23 | 显示全部楼层
2018-01-02: Rosetta@Home, 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....


-------------
2018.01.02 《时代》周刊近期发表了一篇关于David Baker 与Rosetta 的文章

《科学家正在为你的身体设计蛋白质》  https://www.nytimes.com/2017/12/ ... gn-david-baker.html

人类的身体中能够合成上万种细胞蛋白,每一种都有他们各自的任务。现在,研究者们已经掌握了自行创造全新蛋白质的力量。。。

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zhouxiaobo + 15 啊,刚发完weibo才看到这条。(.
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