[BOINC] [生命科学类] Rosetta@home

Youth

Posted 1 Dec 2006 7:33:55 UTC

I'm just back from the CASP7 meeting which was very exciting. I will give a fuller report this weekend after I catch up on sleep and the pile of things which has accumulated, but very briefly it turns out that many of the predictions Rhiju and Bin have posted on the "top predictions" page were the best made for these targets in the whole prediction experiment, and for the experts among you, the T283 ab initio prediction was found by the CASP7 assessor to be accurate enough to unambigously solve (by molecular replacement) the xray crystallography phase problem, an absolutely unprecedented result.

看来今年CASP7上Rosetta@Home的表现真是相当不错！

Youth

Posted 4 Dec 2006 3:00:18 UTC
Last modified: 4 Dec 2006 7:31:08 UTC  

Thanks to feet1st for clarifying my original post! His improved version, with an explanation suggested by SOAN, follows:

The assessor reports are not yet posted. In the mean time, you can get an overview of the predictions you all made for CASP7 by looking at this url

Each team participanting in CASP is allowed to submit up to 5 models. You can see each of our submitted models indicated by black lines. The orange lines are the models submitted by some of the other 252 groups that participated in CASP7. Not all groups submitted predictions for all of the proteins.

The y axis is a measure (RMSD) of how close the model is to the true structure for the fraction of the structure indicated on the x axis (from 0 to 100%). Each point (X,Y) on one of the lines indicates that that the best predicted contiguous segment of X percent of the residues in the model represented by the line was on average Y angstroms from the experimentally determined structure. .

A perfect prediction would be a horizontal line at zero. so we would like there to be at least one black line at zero all the way accross for each target (there are five black lines in each graph, one for each of the five models submitted). The first thing to note is that we are not even close to predicting protein structures perfectly! This is why we are continuing to do methods development work as a major part of Rosetta@Home, and we think the predictions would be better if they were made today than these which we made last summer. Thanks again for contributing to our efforts.

How did Baker lab do compared to the 252 other groups participating in the CASP7 experiment? One way to look at this is to count the number of times one of the Rosetta@Home models was clearly better than the models produced by other groups. You could then browse through each of the graphs, and count the number of cases one of the black lines is clearly lower than all of the orange lines for some fraction of the structure.

My son Benjamin and I just did this quickly. Our list is the following:
targets
283
299
299D1
299D2
300
307
316D3
319
323
327
329
330
330D2
331
347D2
350
354
356
357
360
363
365
368
380

From looking at these plots, it does not seem other groups had as many "breakaway" models. If you have a minute, take a look at these plots and perhaps select a different group to see what their plots look like.

Also note that when our predictions are not clearly better then the others, we're often very close to the best predictions. This is indicative of Rosetta's consistently good predictions.

This "numerical evaluation" is only part of the story, and the measure used in these plots only looks at the position of the backbone Calpha atoms, not at the protein sidechains which, as you know, we spent a lot of time modeling as well. I'll give you a report on the expert evaluation and the results for the whole protein chain including sidechains in a day or two.

http://www2.predictioncenter.org ... =ALL&MODE=TABLE

Youth

Posted 4 Jan 2007 16:43:18 UTC by David Baker

Happy New Year to all! 2007 should be a very exciting year at rosetta@home!

Continuing the theme of my last post, I just met with Barbara Wakimoto, who leads a group at the UW
which trains science teachers (see http://monera.biology.washington.edu/hhmi/), and I just submitted a proposal to HHMI to develop a curriculum unit arounds rosetta@home for middle school and high school and later with direct input and feedback from teachers. There are a lot of excellent materials already available on the internet, so what we will mainly need to do is to collect the most appropriate information and assemble it. If you have ideas, perhaps a thread could be started on these boards with useful links. Of course, once these materials are asssembled coherently, it should be an ideal way for newcomers to learn about the science underlying rosetta@home.

准备把rosetta@home引入到中学的课程中。

In another news, I just put the final touches on the paper describing the first round of results from the rosetta WCG project led by my former graduate student Richard Bonneau who is now a professor at NYU. This paper is going to be published in a very successful relatively new journal called Public Library of Science, which is based on the premise that all research results should be freely available to everybody, and hence there are no subscription fees; anybody can freely look at all the papers they publish. I'll put up the link to the paper as soon as it appears so you can see how this works.

一篇关于rosetta WCG项目研究结果的文章将发表在一份相对较新的期刊《Public Library of Science》上，这份期刊的宗旨是所有的研究结果都将对任何人公开！

Youth

有一段时间没算rosetta，今天才发现官方网站的用户页面上多了个“Reports and plots of results from active work units”的链接，可以查看最近完成的任务包的预测结果（和其他用户的预测结果相比较是个什么情况之类的），顺便发现项目方使用了m$的sqlserver2005：）

Youth

Posted 5 Feb 2007 5:48:12 UTC  

We are just finalizing two manuscripts which describe some of the most exciting results obtained thus far by rosetta@home. We have identified the rosetta@home contributors who found the rather spectacular low energy structures reported in the first paper, and would like to acknowledge them in the paper. Our question is whether to acknowledge these contributions through usernames or real names, and we certainly don't want to use the latter without permission. Here are the user names of the four participants for the first paper, I'll post the participants we would like to acknowledge in the second paper when we have identified them.

78884 aotama
66651 DJ N-4ceR
77194 DOJ F@T Elvis Clan
49841 Vroomfondel

It would be great if the above participants could let us know how they would like to be acknowledged.

这种对用户贡献的肯定方式还是不错的，有兴趣的同学加油算吧，不定哪天你的名字也能上paper了：）

Youth

http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1177

Posted 6 Feb 2007 5:38:23 UTC  
Yesterday I acknowledged the participants who found the low energy structures being reported in Rhiju's paper. Today I have a list of the participants who found the low energy structures for the proteins reported in Bin's paper (the list is longer because Bin's paper describes a number of different proteins, we are citing the four participants who found the lowest energy structures for each of them). Again, please let us know how you would like to be acknowledged.

33706 gibsonrr
22840 Jynxedu
93320 John Michael Hess
59655 Luke

66275 Marko
757 Ian_D
82740 pxee
42892 csbyrosetta

96970 Allan Staib
97036 TJSwan
80380 Yunomi
7028 Etienne Guyot

31134 GeorgeF
68333 Jarom Smith
9221 UBT - Menace
62362 Boštjan Rudolf

17199 [SETI.USA] D. Brown
90304 bs98909
86711 papagoof
76056 Ackiss

86743 Noel E. Shea
58129 Bjarke.Orbeck
2446 SerVal
55755 Erik

33464 [DPC]FOKschaap~devzero
44026 A's Team
13172 jeidler
9030 Rebel Alliance

大家看看有没有自己，有的话可以去报个到了：）

lch=gta

Mon, 23 Jul 2007 07:00:00 GMT
Rosetta@home has been updated to version 5.72. This version includes some new features that will let us test variations of the energy function for proteins and RNA. For details, see this thread.


2007.7.23
大意：

Rosetta@home更新至5.72。这个版本包含了新特性，使得我们可以测试蛋白质和核酸的能量函数的变化。

Julian_Yuen

July 30, 2007
Update: R@H had been moved over to the fiber SAN.... more details here.

July 31, 2007
Rosetta@home has been updated to version 5.72. This version fixes an issue in high resolution modeling of RNA. For details, see this thread.

[ 本帖最后由 Julian_Yuen 于 2007-8-1 11:34 编辑 ]

Julian_Yuen

down机预告~

September 6, 2007
Outage Notice: The project is down for repairs. The SAN suffered a serious hardware fault and we're rebuilding the filesystem upon which the R@H project is stored. We're working as quickly as we can to get things back up and running.....

老冬腌菜

Sep 18, 2007
The project is back online.
项目恢复


Sep 18, 2007
Outage Notice: The project will be down today from around 2pm to 5pm PST for maintenance.
项目维护停机


Sep 18, 2007
Update: The RAID is rebuilt and now we're chasing down the next bottleneck....
磁盘阵列已被重建，我们正在寻找下一个瓶颈


Sep 13, 2007
Problems solved! Rosetta@home has been updated to version 5.80. This version contains support for having small molecules present in protein-protein docking simulations. This is used in the current round of Capri. For details, see this thread.
问题解决！Rosetta@home 客户端已升级至 5.80 版。这个版本包含了对小分子蛋白质之间的影响（？）进行模拟的支持。


Sep 13, 2007
Rosetta@home is currently down due to a technical problem. We are working on a solution.
Rosetta@home 因技术问题停机


Sep 8, 2007
Rosetta@home has experienced a horrendous hardware/fireware failure. We essentially lost the SAN partition upon which the project was running...for details see the technical news.
Rosetta@home 经历了一次可怕的硬件或者防火墙故障。我们丢失了当前运行的 SAN 项目的数据。


Sep 2, 2007
Rosetta@home has been updated to version 5.78. This version includes some small but useful updates for RNA folding simulations and some special symmetric folding runs as well. For details, see this thread.
Rosetta@home 客户端升级至 5.78 版。这个版本包含了一些对于RNA折叠模拟项目小但是有用的升级，同时提供了对一些特别的平衡（？）折叠任务的支持。

Aug 29, 2007
Rosetta@home experienced an unannounced, albeit planned, outage today at 8AM. For details see the technical news.
Rosetta@home 在今天早上8点 (gmt?) 经历了一次没有声明的（虽然是计划的）断粮。

Aug 21, 2007
Rosetta@home has been updated to version 5.77. The stable release has also been updated to 5.69. Both versions include a bug fix involving the scoring logic for closing chainbreaks. Please report any bugs in this thread.
Rosetta@home 客户端升级至 5.77 版。稳定版 v5.69 也已经发布。两个版本都包修复了一些bug。

Aug 12, 2007
Rosetta@home has been updated to version 5.76. This version includes updates for the RNA high resolution mode and for protein workunits that involve enforcing strand pairs and then closing accompanying chain breaks ('jumping'). For details, see this thread.
Rosetta@home 计算程序升级至 5.77 版。

Youth

好久没更新了

Posted 16 Aug 2007 6:04:32 UTC

The first game prototype is now online! we've put almost all of our efforts into a much more sophisticated version in which the game player collaborates with his/her computer and other players to solve difficult problems, but as an intro Ian Davis has put together a simple Java version that you can play without downloading anything on to your computer. we hope to build this into a fun way to explain the science we are doing on rosetta@home and as a warm up to the multiplayer human + computer version. Here is Ian's recent post, which you can also find on a thread he just started elsewhere on these pages:

Hi R@H community,

I've been working with several others in the lab on an "interactive Rosetta" project. The vision is that one day, you'll be able to interact with Rosetta as it runs, both (1) to help it produce better results and (2) to learn about what it's doing.

We're not there yet, but we have an early prototype for #2, the educational side. This is a simple "game" you can play in your web browser (using Java) to find the missing side chain for a designed protein that might be used to fight cancer. In this case, there's a small number of choices and the right answer should be obvious. However, it illustrates one of the basic steps that Rosetta performs thousands of times every time it designs a protein.

More "levels" for the game will be coming in the future. Also we're already planning to change the interface on the Java applet and to add a "score board" so you can compete against others, but if you try it out and have other comments or ideas to share, please post them here.

Here's the link: the Rotamer Game

http://boinc.bakerlab.org/rosetta/rah_misc/king_rotamer_game/

交互版本的Rosetta@home演示原型。

Youth

Posted 8 Oct 2007 4:27:01 UTC

We have made huge progress with the interactive video game version of rosetta. We are on our sixth trial so far, with many improvements being made at each step. in the most recent trials, a subset of the people who have tried have become hooked and played (competitively) for many hours in a row. our goal now is to increase the fraction of people who get really into the game by adding animations and other information at the beginning to help guide people starting to play for the first time.
Within the next month I will be asking for volunteers for a more general trial. The reason for all of the trials is that we want to have the game really perfect before it goes fully public. Again, the two main goals are (1) educational--I'm convinced that people playing the game will gain a huge amount of insight into what biomolecules are and how they work and (2) research--we think people playing the game may be able to find much lower energy structures than the computer working on its own. time will tell!

开发交互版本的Rosetta@home已经有了很大的进展，但仍在努力改进中，以期待能在正式发布时更加完美。该工作的主要目的一方面是教育，可以让大家对分子生物学有更深入的了解，另一方面是科研，我们认为玩这个游戏的人会比计算机更容易找到最低能量结构。

On the science side, we are just completing two manuscripts describing landmarks in molecular biology: the design of novel enzymes (using computational protein design and rosetta@home) that catalyze chemcial reactions for which there are no naturally ocurring catalysts. (perhaps one of the experts among you can explain what this means on the "discussion" thread). I presented this work at two recent scientific meetings and people were pretty blown away. This opens the door to creating new catalysts for all sorts of chemical reactions that are difficult currently or require toxic or environmentally unfriendly reaction conditions.

又有两篇论文在准备中。

cnchina

We are currently down for maintenance. We hope to be back online later this evening.

Sorry for any inconvenience.


今天（07年11月10日）停機維護。今晚（明晨）可能會恢復。

kimiwa

继续关注！

Youth

Posted 21 Nov 2007 6:00:17 UTC

We have been working hard on a new streamlined version of rosetta which will soon be running on rosetta@home. there are so many developers of rosetta that the code grew very large and somewhat disorganized, and several members of the rosetta develpment community took it upon themselves to write from scratch a modern completely object oriented version. many others have joined in more recently, and the new version is now almost up to speed. we can tackle some new problems with this new code, as well as all of the old ones, so we will be gradually transitioning over in the next six months.

我们正加紧进度准备一个新的流水线化的rosetta版本，这个版本将很快出现在rosetta@home上。因为之前rosetta的开发人员非常多，导致代码非常庞大而且组织混乱，因此rosetta社区的几位成员从头开始编写了这个新的完全面向对象的版本。许多其它成员最近也加入了进来。接下来的六个月将是过度期，新旧版本程序的问题我们都会处理。

among the new things to come in the relatively near future include virtual drug screening by large scale docking of small molecules onto protein targets. accurately docking even a single small molecue onto a protien target is fairly computationally intensive, so if we want to dock 100 or 1000 possible drug candidates onto a protein target large scale computing will definitely be critical.

介绍近期将要加入的项目内容，本人专业知识太差，不好翻译了...只知道需要大量的计算力，和药物设计相关。