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[独立平台] [生命科学类] Folding@Home

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 楼主| 发表于 2016-11-11 09:14:17 | 显示全部楼层
Stats System Down Temporarily
November 9, 2016 by Carlos Hernández ·
We’re experiencing some technical issues with one of our client-side servers (fah-web.stanford.edu).  Stanford IT is working hard to get things working again, but in the meantime individual and team points data might not be accessible (however all work units should receive credit). We’ll post an update as soon as things are up and running again.
大意:
统计系统挂了,维护人员正在修,积分暂时无法更新(积分都记了不会少给的)

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 楼主| 发表于 2017-1-31 23:51:09 | 显示全部楼层
Release: New core 21 v.0.0.18 with support for Nvidia drivers 375.57+
January 30, 2017 by thynell ·
We are pleased to announce the release of core 21 v0.0.18 to full FAH. The updated core will be pushed out automatically for both windows and linux donors over the next week as projects are updated to require this min-core-version.

This release contains a workaround for a change made in the NVIDIA OpenCL driver introduced in drivers starting with 375.57, as well as some improvements to error handling codes.

While a slight reduction in performance may be observed, this performance regression should be eliminated when NVIDIA removes the hotfix in forthcoming driver updates.

There is a known issue that this release will, for some projects, print sporadic messages to the log due to a known visualizer bug:

05:34:52:WARNING:FS01:Size of positions 64914 does not match topology 19

This issue does not affect the quality of the science, and a workaround is already in testing for v0.0.19, which we hope to release in a week.

Thank you all for your patience.

Kindly report issues here:

https://foldingforum.org/viewtopic.php?f=24&t=29633

~ The FAH Core 21 crew
大意:
发布v0.0.18新版GPU core。下周会随项目设置更新。
新内核解决了N卡自375.57版OPENCL驱动引入的问题。虽然性能暂时回降低,但待N卡后面更新驱动后,性能还会升回来。
已知问题:log中偶尔会报错。
但仅仅是日志打印并不会对计算产生影响。内测中的v0.0.19解决了这个问题,大概一周内发布新版。
 楼主| 发表于 2017-5-25 10:06:09 | 显示全部楼层
本帖最后由 vmzy 于 2017-5-25 10:49 编辑

FOLDING@HOME SERVERS MAINTENANCE SCHEDULED SHUTDOWN JULY 6& 7TH, 2016
May 24, 2017
by Theresa Derner

Hello Everyone,

SERVERS DOWN JULY 6 & 7

The Stanford Research Computing Facility hosting some of our key Folding@home servers will be carrying a maintenance to their electricity system on Thursday & Friday, July 6 &7th. We expect F@H to be down those days. So please prepare for outage. Sorry for the inconvenience it may cause!

Best,

Folding at Home team!
大意:
FAH计划于7月6-7日进行电力设备检修,届时FAH全站下线,请大家做好准备。

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 楼主| 发表于 2017-7-6 11:06:16 | 显示全部楼层
JULY 6th &7th, 2017 F@H servers Down all day
Postby TDPanda1*COStaf » Thu Jul 06, 2017 3:17 am

Hello Everyone,

SERVERS DOWN JULY 6 & 7,2017

The Stanford Research Computing Facility hosting some of our key Folding@home servers will be carrying a maintenance to their electricity system on Thursday & Friday, July 6 &7th. We expect F@H to be down those days. So please prepare for outage. Sorry for the inconvenience it may cause!

Plus we are working on the Member Certificate issues. Thanks for your patience.

Best,

Folding at Home team!
大意:
再次提醒,斯坦福计算中心,进行电力设备检修。FAH服务器这两天可能会宕机下线。

点评

辛苦费 (「・ω・): 5.0
辛苦费 (「・ω・): 5
  发表于 2017-7-7 17:09
发表于 2017-12-4 18:35:03 | 显示全部楼层
New (GRO A4) projects 14041 and 14042 to ADV
Postby yunhui » Wed Nov 29, 2017 6:22 pm

Releasing new SMP A4 (GRO_A4) projects p14041 and p14042 to ADV. These are exactly the same as projects p13717 and p13179, but adaptive sampling from those two old projects. These are being served from vav4.ocis.temple.edu (155.247.166.220).
Description here: http://fah-web.stanford.edu/cgi-bin/fahproject.overusingIPswillbebanned?p=13717

Project: 14041
stats credit: 996
timeout: 15.2
deadline 33.3
k-factor v=0.75
number of atoms: 30404


Project: 14042
stats credit: 994
timeout: 15.2
deadline 33.2
k-factor v=0.75
number of atoms: 30347
yunhui

Disease Type: Unspecified

Phenylalanine Hydroylase (PAH) functions to keep the essential amino acid phenylalanine (Phe) below levels that cause irreversible brain damage in infancy/childhood and behavioral problems throughout life.  Mutations to the PAH genes can disrupt this control function and cause phenylketonuria (PKU), which occurs in about 1:12000 live births.  Due to mandatory screening, PKU is typically diagnosed at birth and successfully treated with strict dietary control of protein intake.  However, adults living with PKU need a less restricted diet and new therapies are sought.  Such therapies can come from understanding how PAH works.

Until very recently, the way that PAH controls Phe was poorly understood.  However, new research reveals important details about how PAH changes its shape in order to control its enzymatic activity (1, 2).  Our goal in this project is to use molecular simulation to understand the PAH shape changes that accompany activation in response to elevated levels of Phe and how this process is perturbed in disease.

A4多核包14041、14042转移至ADV(参数下接包)。项目的研究目的:苯丙氨酸羟化酶(PAH)的基因突变会导致人体必备氨基酸苯丙氨酸(Phe)在婴儿及儿童时期的含量低下,造成不可逆的脑损伤,苯丙酮尿​​症的发病概率在1:12000。新的研究表明PAH会改变其形状以控制其酶活性,项目便研究 Phe 水平的升高对疾病的影响导致PAH的变化。



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yimu35 + 12 辛苦了!

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发表于 2018-2-10 16:02:05 | 显示全部楼层
TRAINING AND VALIDATION OF A LIQUID-CRYSTALLINE PHOSPHOLIPID BILAYER FORCE FIELD.
February 6, 2018
by Anton Thynell

Related Articles
Training and Validation of a Liquid-Crystalline Phospholipid Bilayer Force Field.

J Chem Theory Comput. 2016 Dec 13;12(12):5960-5967

Authors: McKiernan KA, Wang LP, Pande VS

Abstract
We present a united-atom model (gb-fb15) for the molecular dynamics simulation of hydrated liquid-crystalline dipalmitoylphosphatidylcholine (DPPC) phospholipid bilayers. This model was constructed through the parameter-space minimization of a regularized least-squares objective function via the ForceBalance method. The objective function was computed using a training set of experimental bilayer area per lipid and deuterium order parameter. This model was validated by comparison to experimental volume per lipid, X-ray scattering form factor, thermal area expansivity, area compressibility modulus, and lipid lateral diffusion coefficient. These comparisons demonstrate that gb-fb15 is robust to temperature variation and an improvement over the original model for both the training and validation properties.

发表于 2018-3-25 10:23:56 | 显示全部楼层
TRANSFERABLE NEURAL NETWORKS FOR ENHANCED SAMPLING OF PROTEIN DYNAMICS.
March 12, 2018
by Anton Thynell

Transferable neural networks for enhanced sampling of protein dynamics.

J Chem Theory Comput. 2018 Mar 12;:

Authors: Sultan MM, Wayment-Steele HK, Pande VS

Abstract
Variational auto-encoder frameworks have demonstrated success in reducing complex nonlinear dynamics in molecular simulation to a single non-linear embedding. In this work, we illustrate how this non-linear latent embedding can be used as a collective variable for enhanced sampling, and present a simple modification that allows us to rapidly perform sampling in multiple related systems. We first demonstrate our method is able to describe the effects of force field changes in capped alanine dipeptide after learning a model using AMBER99. We further provide a simple extension to variational dynamics encoders that allows the model to be trained in a more efficient manner on larger systems by encoding the outputs of a linear transformation using time-structure based independent component analysis (tICA). Using this technique, we show how such a model trained for one protein, the WW domain, can efficiently be transferred to perform enhanced sampling on a related mutant protein, the GTT mutation. This method shows promise for its ability to rapidly sample related systems using a single transferable collective variable, enabling us to probe the effects of variation in increasingly large systems of biophysical interest.

PMID: 29529369 [PubMed – as supplied by publisher]

发表于 2018-3-26 14:42:59 | 显示全部楼层
可转移至神经网络增强蛋白质动力学取样。
该法可使我们能够探索越来越复杂的生物物理学系统中对于蛋白质变异的影响。


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发表于 2018-10-22 21:52:52 | 显示全部楼层
Simulations of the regulatory ACT domain of human phenylalanine hydroxylase unveil its mechanism of phenylalanine binding.

J Biol Chem. 2018 Oct 04;:

Authors: Ge Y, Borne E, Stewart S, Hansen MR, Arturo EC, Jaffe EK, Voelz VA

Abstract
Phenylalanine hydroxylase (PAH) regulates phenylalanine (Phe) levels in mammals to prevent neurotoxicity resulting from high Phe concentrations as observed in genetic disorders leading to hyperphenylalaninemia and phenylketonuria. PAH senses elevated Phe concentrations by transient allosteric Phe binding to a protein-protein interface between ACT domains of different subunits in a PAH tetramer. This interface is present in an activated PAH tetramer (A-PAH) and absent in a resting-state PAH tetramer (RS-PAH). To investigate this allosteric sensing mechanism, here we used the GROMACS molecular dynamics simulation suite on the Folding@home computing platform to perform extensive molecular simulations and Markov state model (MSM) analysis of Phe binding to ACT domain dimers. These simulations strongly implicated a conformational selection mechanism for Phe association with ACT domain dimers and revealed protein motions that act as a gating mechanism for Phe binding. The MSMs also illuminate a highly mobile hairpin loop, consistent with experimental findings also presented here that the PAH variant L72W does not shift the PAH structural equilibrium toward the activated state. Finally, simulations of ACT domain monomers are presented, in which spontaneous transitions between resting-state and activated conformations are observed, also consistent with a mechanism of conformational selection. These mechanistic details provide detailed insight into the regulation of PAH activation and provide testable hypotheses for the development of new allosteric effectors to correct structural and functional defects in PAH.

PMID: 30287685 [PubMed – as supplied by publisher]


-----------------
标题:对人类苯丙氨酸羟化酶中调控ACT结构域的模拟揭示了这种酶与苯丙氨酸的结合机制
摘要:苯丙氨酸羟化酶(PAH)是哺乳动物体内的一种非常重要的酶,它能够调节动物体内的苯丙氨酸(Phe)含量,从而防止过高苯丙氨酸浓度产生的神经毒性对动物造成伤害(由基因失调导致的高苯丙氨酸血症以及苯丙酮酸尿症就是苯丙氨酸羟化酶异常的结果)。四聚体①苯丙氨酸羟化酶②可以通过迅速的变构③在两个亚基④的ACT结构域⑤之间形成一个蛋白质交互界面(protein-protein interface),并通过这个界面与苯丙氨酸的结合,从而感知苯丙氨酸浓度的变化。这个界面只存在于被激活的四聚体苯丙氨酸羟化酶(A-PAH)中,而在处于休眠状态的四聚体苯丙氨酸羟化酶(RS-PAH)却不存在。为了研究这种变构感知的机制,我们在这里使用了Folding@home 计算平台的GROMACS 分子动力学模拟工具,进行了广泛的分子模拟和对苯丙氨酸与ACT结构域二聚体结合过程的 Markov state model analysis (具体解释看不懂,这个词在wiki上被重定向到了“隐马尔科夫模型”页面)。这些模拟的结果强烈暗示着在苯丙氨酸与ACT结构域二聚体的反应中有一种蛋白质构象选择机制的存在;同时模拟结果也显示出,在与苯丙氨酸结合的过程中,蛋白质起到了类似闸门的作用。对Markov state model 的分析结果则发现了一条高度灵活的茎环(hairpin )⑥,实验结果表明苯丙氨酸羟化酶的异构体L72W 的结构稳定性并没有向着激活状态改变。最后,对于ACT结构域单聚体的模拟结果:我们观察到,在自发进行的激活-休眠形态转换过程中,同样存在一种构造选择机制。这些机制的发现,让我们对苯丙氨酸羟化酶的激活控制有了更深入的认识,并且为将来开发新变构效应因子(allosteric effectors )、用以修复苯丙氨酸羟化酶的结构与功能性缺陷提供了可试验的假设。

科普:
①四聚体:四聚体为蛋白质四级结构中的一种蛋白质复合物名称,表示“由四个亚基构成的蛋白质”。同理,下文中提到的单聚体即为“由一个亚基构成的蛋白质”。关于亚基的含义,下面的注释有单独的解释。
②四聚体苯丙氨酸羟化酶:原核细胞的苯丙氨酸羟化酶是单聚体,真核生物体内的苯丙氨酸羟化酶则处于四聚体与二聚体的平衡状态[引用1],四聚体是酶高亲和力和搞催化能力的形态,四聚体的特异活性是二聚体的五倍[引用2]。而本文的主要研究对象看起来只限于四聚体苯丙氨酸羟化酶。
③变构:又称别构,即蛋白质结构的改变。在这里,原文实际上描述的是一个“别构调节”的过程,所谓别够调节,简单的理解,就是酶(蛋白质)通过调整自己的结构来改变活性,以起到调节体内某种特定反应速度的作用。
④亚基:指参与组成蛋白质复合物(寡聚体或多聚体)的单个蛋白质分子。一个蛋白质亚基就是一条多肽链,而一条多肽链是由一组基因所编码,这就意味着每个亚基都由一组基因编码。[引用3]
⑤ACT结构域:蛋白质结构域(英语:protein domain)是蛋白质中的一类结构单元,是构成蛋白质(三级)结构的基本单元。[引用4] ACT结构域是一种在蛋白质中非常常见的结构域,它与多种受氨基酸浓度调控的代谢酶有关。它得名于三种含有这种结构域的蛋白质: Aspartate kinase (天冬氨酸激酶), chorismate mutase (分支酸变位酶)和 TyrA (预苯酸脱氢酶)。[引用5]  这种结构能通过精确调整蛋白质的构象提供变构调节。
⑥茎环:茎环(英语:Stem-loop,或译主干-循环)指一种分子内碱基配对方式,与因此形成的结构,可发生于单股DNA,但在RNA分子中较为常见。当形成的循环较小时,也称为发夹(hairpin)或发夹环。[引用5]


因为也不是正式翻译论文,引用格式就不搞那么规范了。。
[引用1] 维基:Phenylalanine hydroxylase条目“Tetramerization domain”部分
[引用2]《苯丙氨酸羟化酶的研究进展》(《生命科学》第25卷 第4期 2013年4月)(实际上,引用的这篇发表于2013年的文章已经在相当程度上解释了这篇项目论文的研究背景)
[引用3]中文维基:蛋白质亚基
[引用4]中文维基:蛋白质结构域
[引用5]维基:ACT domain
[引用5]中文维基:茎环

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 楼主| 发表于 2019-10-8 10:12:41 | 显示全部楼层
BONUS RECREDIT
October 7, 2019
by Greg Bowman

This past June, a server error led to a failure to assign bonus points to a number of work units. We corrected the error as soon as it was detected. Now we have identified the work units that were impacted. Recredits will take place over the next few days. To all those who were affected, thank you for your patience.
大意:
经查今年6月有一个服务器出错,有很多任务包没有发奖励积分,接下来几天我们会给这些任务包补发奖励积分。
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