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Discussion in 'Folding@Home - Join Team Guru3D !' started by PantherX, Jun 1, 2010.

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iancook221188 Ancient Guru

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OpenMM webinar
February 10, 2014 by Vijay Pande ·

I recently gave a webinar on OpenMM, the heart of our Core17 for GPUs (and also now more recently, high performance computing on multi-core CPUs as well). Here’s a link if you’re curious to learn more:

http://on-demand.gputechconf.com/gtc/2014/webinar/gtc-express-openmm-webinar.mp4
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iancook221188, Feb 16, 2014

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iancook221188 Ancient Guru

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Update to stats system accounting of ATI GPUs
February 17, 2014 by Vijay Pande ·

We’ve been suspicious that the stats system has been undercounting ATI/AMD GPUs for some time now and we have found the issue. We’ve rolled out an update to the stats code and so we expect to see more ATI GPUs showing up in osstats.
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iancook221188, Feb 19, 2014

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Registration open for a free webinar: The Next Steps for Folding@home
February 18, 2014 by Vijay Pande ·

I’ll be presenting a webinar on Folding@home open to the public on Tuesday, May 27, 2014 9:00 AM – 10:00 AM PDT. You can register on this link: https://www2.gotomeeting.com/register/688201986. The goals are to talk about what we’ve been able to do so far and where we’re going.

Summary. Folding@home is a large-scale volunteer distributed computing project, started in October 1, 2000. For over a decade, new types of hardware (such as GPUs, multi-core CPUs, and PS3) and algorithms have been pioneered in order to make significant advances in our ability to simulate diseases at the molecular scale. Join Professor Vijay Pande from Stanford University for a brief introduction to the goals of Folding@home, followed by the successes so far. Prof. Pande will end with a discussion of what’s being done today, as well as the plans for greatly enhancing what Folding@home can do through new initiatives currently under way.

Please note that this webinar starts at 9:00 AM Pacific, 12:00 PM Eastern, and 5:00 PM BST.
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iancook221188, Feb 19, 2014

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FAH at Biophysical Society
February 24, 2014 by Greg Bowman ·

The Biophysical Society, an international group that brings together researchers taking a physical perspective on biology, just had its annual meeting in San Francisco. A number of us involved with Folding@home gave talks and/or posters and there was tremendous interest in what we’re doing. So, thanks to all of you for your help in facilitating great science!
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iancook221188, Mar 1, 2014

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New FAH research in Cancer published in Nature Communications
March 5, 2014 by Vijay Pande ·

Our paper “Activation pathway of Src kinase reveals intermediate states as targets for drug design” in Nature Communications has just come out. As with Nature journals, it’s unfortunately behind a pay wall, but per NIH rules, it will become open access in a year. The key results in this paper is the use of FAH simulations to understand a key protein target in cancer (src kinase), especially to find new ways to target it for novel drug design.

A more technical summary is given in our abstract:

Unregulated activation of Src kinases leads to aberrant signaling, uncontrolled growth and differentiation of cancerous cells. Reaching a complete mechanistic understanding of large-scale conformational transformations underlying the activation of kinases could greatly help in the development of therapeutic drugs for the treatment of these pathologies. In principle, the nature of conformational transition could be modeled in silico via atomistic molecular dynamics simulations, although this is very challenging because of the long activation timescales. Here we employ a computational paradigm that couples transition pathway techniques and Markov state model-based massively distributed simulations for mapping the conformational landscape of c-src tyrosine kinase. The computations provide the thermodynamics and kinetics of kinase activation for the first time, and help identify key structural intermediates. Furthermore, the presence of a novel allosteric site in an intermediate state of c-src that could be potentially used for drug design is predicted.
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iancook221188, Mar 5, 2014

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iancook221188 Ancient Guru

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Making dramatic improvements to the models used to study proteins
March 6, 2014 by Vijay Pande ·

In our simulations, we use models (aka “force fields”) of how a protein’s atoms interact physically. Recently, we’ve made an important advance in how to make these models, which will, in time, have a huge positive impact on Folding@home’s ability to make even more accurate predictions.

You can see a story on it in BCR and the full paper in the journal’s site.
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iancook221188, Mar 8, 2014

#266
iancook221188 Ancient Guru

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Bryostatin and Projects 9000-9015
November 5, 2014 by Mark Piercy ·

Steven Ryckbosch, a graduate student in the Pande Group recently presented his work on Bryostatin. Folding@home projects 9000-9015 are running simulations to help answer the questions he has about it’s structure and function.

Bryostatin is a naturally occurring marine molecule that shows promising and unique activity against several diseases (most notably, cancer, HIV/AIDS, HIV latency, and Alzheimer’s). Its main target, protein kinase C (PKC), is a signaling protein central to many cellular functions. In its active form, PKC binds its ligand and is associated with the cell membrane, but we currently lack structural information about this complex in its membrane microenvironment.

The simulations performed on FAH will help to provide a structure to the PKC-ligand-membrane complex. This is complicated by the fact that while other compounds such as the phorbol esters also bind to PKC, they exhibit extremely different effects in cells and organisms. The structure and dynamics of this complex would allow us to understand bryostatin and other ligands’ binding mode and thus how to modify and tune it’s structure to improve function or even create new functions as needed for new therapies in the clinic.

Some questions Steven and the group are trying to answer:

How can we use simulation to find protein-membrane structures?
How can ligands modulate protein-membrane interaction?
How are membranes affecting bryostatin function?
How can this inform our design of new bryostatin analogues?

Below is a molecular simulation model of bryostatin bound to PKC’s active site.

Last edited: Nov 7, 2014

iancook221188, Nov 6, 2014

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iancook221188 Ancient Guru

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Ab initio nanoreactor discovers new reaction pathways
November 7, 2014 by Mark Piercy ·

Some very exciting research by Pande Group members Lee-Ping Wang and Robert McGibbon in collaboration with the Martinez Lab was recently published in Nature Chemistry. They report the development and application of the ab initio nanoreactor—a highly accelerated first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms.

Using the nanoreactor, they showed new pathways for the amino acid glycine’s synthesis from primitive compounds proposed to exist on the early Earth, which provide new insight into the classic Urey–Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery.

The nanoreactor simulations were made possible by GPUs and the TeraChem quantum chemistry software; these technologies accelerate the calculation over conventional CPU codes by 10-100x.

Below is the nanoreactor simulation of the classic Urey–Miller experiment.

https://www.youtube.com/watch?v=WHQn03ZiqKY
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iancook221188, Nov 7, 2014

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iancook221188 Ancient Guru

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A discussion of recent FAH work on ab initio nanoreactor
November 14, 2014 by Jingcheng Wu ·

What’s an ab initio nanoreactor for?

In an ab initio nanoreactor, molecules are allowed to react freely with each other over the course of the molecular dynamics simulation, and then we observe what products come out of it and how the products were formed. Besides obeying the fundamental laws of physics, no additional assumptions were imposed to the system, hence ab initio.

The number of reactant molecules used to seed the simulations was small (50-100 molecules) compared to the number of molecules typically used in experimental methods, but is nonetheless very large from the standpoint of quantum chemistry calculations. To make the reactions occur more rapidly, we periodically push the molecules to the center of the ab initio nanoreactor with a virtual piston. What this does is to make the molecules bump into one another more frequently, and also provide the energy required for certain reactions to take place.

The significance of ab initio nanoreator

Traditionally, experimental methods are heavily relied on to discover new molecules and reaction pathways, and computational methods mainly played a supportive role to complement experimental methods. The results of this study prove that computational methods can also play the leading role in discovery, and can help guide experimental methods by posing new hypotheses and suggesting which experiments to do. It’s especially useful for detecting complex chemical reactions where several things happen at the same step during the reaction process that’s hard to detect via experiments.

The potential applications of ab initio nanoreactors are broad. Because of the ab initio approach coupled with some refinement methods and automatic analysis, we can achieve the goal of discovering new molecules, new reaction pathways and mechanisms in many different settings and environments. For instance, it could contribute to out future understanding of the origin of life, birth of stars, means to increase the rate of chemical reactions, earth’s atmosphere, etc.

Results of the study

We carried out two ab initio nanoreactor simulations. The first simulation started with purely acetylene molecules, and we call it acetylene nanoreactor. The second simulation started with a mixture of chemicals postulated to exist in the early earth atmosphere. The second simulation is the computational version of a famous experiment conducted in 1952 (Urey-Miller experiment) that showed complex building blocks of life could form from simple inorganic molecules (1). We call the second simulation Urey-Miller nanoreactor.

For the acetylene nanoreactor, nearly 100 distinct products were formed after ~500 picoseconds simulation time. Many of these product molecules are large (up to over 70 atoms) due to the tendency of acetylene molecules to form long chains and 3D networks. These products are also diverse, for example some have rings some don’t; some are linear some are branched. After comparing our results with those of previous experiments, we found that the acetylene nanoreactor produced not only similar products, but also new products (2, 3).

For the Urey-Miller nanoreactor, the products were relatively small (up to 16 atoms). Among the discovered products, we have amino acids (which are what proteins consist of), urea (participating in metabolism, and the first byproduct of life to be synthesized in the lab) and a bunch of other molecules, all of which have also been detected in meteorites that may have delivered organic molecules to the early earth (4). Many of these molecules are also found in interstellar clouds (5). In addition to the high diversity of products, the Urey-Miller nanoreactor also identified a complex network of reactions (more than 700 distinct reactions). A significant fraction of these reactions are viable in the common environment we live in. Moreover, we found out that water and ammonia allow reactions to proceed faster with less energy for many of these reactions. Last but not least, hydrogen was found rarely involved in the synthesis of a naturally occurring amino acid, glycine, which supports previous proposals that molecules that tend to lose electrons (including hydrogen) don’t participate in biomolecule formations (4).

Method of analysis

To derive insight from a complex network of reactions, we focus on a particular molecule in the network and investigate the reactions it’s involved in, either it’s the product or the reactant. In this way, it allows us to trace the synthetic pathways that lead from the starting molecules. There could be several different pathways to get from the starting material to our molecule of interest. Some intermediate molecules are more common than the others among these distinct pathways.

References

(1) Miller, S. L. & Urey, H.C. Organic Compound Synthesis on the Primitive Earth. Science 130, 245-251 (1959). Doi: 10.1126/science.130.3370.245

(2) Trout, C.C. & Badding, J.V. Solid State Polymerization of Acetylene at High Pressure and Low Temperature. J. Phys. Chem. A 104, 8142-8145 (2000).

(3) Saka****a, M., Yamawaki H. & Aoki, K. FT-IR Study of the Solid State Polymerization of Acetylene Under Pressure. J. Phys. Chem. 100, 9943-9947 (1996).

(4) Danger, G., Plasson, R. & Pascal R. Pathways For the Formation and Evolution of Peptides in Prebiotic Environments. Chem. Soc. Rev. 41, 5416-5429 (2012).

(5) Menten, K. M. & Wyrowski, F. in Sterstellar Molecules: Their Laboratory and Interstellar Habitat (eds Yamada, K. M. T. & Winnewisser, G.) 27-42 (Springer Tracts in Modern Physics 241, Springer, 2011).

Everything else described here is from Wang, L. P., Titov, A. McGibbon, R., Liu, F., Pande, V. S. & Martinez, T. J. Discovering Chemistry With An ab initio Nanoreactor. Nature Chemistry. 2014. Doi: 10.1038/nchem.2099. The article can also be read about on Nov 10th issue of C&E News: http://cen.acs.org/articles/92/i45/Simulation-Technique-Finds-Reaction-Products.html
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iancook221188, Nov 16, 2014

#269
iancook221188 Ancient Guru

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Breast Cancer and Her2 Kinase: Projects 9104-9114
November 20, 2014 by Mark Piercy ·

We are continuing to make a big push into studying cancer. Next up, is work relevant for breast cancer. Specifically, we have started to study the Her2 Kinase, a part of the EGFR family of Tyrosine kinases, responsible for initiating a host of biochemical pathways. These kinases are critical for regulating cell division and thus mutations within the EGFR family have been linked to various types of cancers, including breast and pancreatic cancer.

The aim of projects 9104 to 9114 is to understand the effect of certain mutations in the kinase domain of Her2. We are also hoping to find new druggable states within the system for creating the next generation of targeted cancer therapeutics, as well as to study the effect of mutations, which will give us insight into mutations present in breast cancer tumors.

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iancook221188, Nov 21, 2014

#270
iancook221188 Ancient Guru

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Support from NVIDIA’s Compute the Cure
November 24, 2014 by Vijay Pande ·

I’m happy to announce that Folding@home has been awarded a Compute The Cure Award from NVIDIA. Their financial support will help build key new infrastructure in Folding@home as well as support our science efforts. You can see more in their announcement.
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iancook221188, Nov 25, 2014

#271
iancook221188 Ancient Guru

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Exploring how mutations affect folding using Markov State Models
November 25, 2014 by Vincent Voelz ·

A powerful method to understand folding and conformational change in proteins has been the Markov State Model (MSM) approach, in which protein dynamics can be described as a network of conformational states connected by forward and backward transition rates. Folding@home has proved to be an extremely valuable tool for constructing MSMs, because large-scale simulations are needed to sample the relevant states (numbering in the tens of thousands or more) and estimate the rates (by observing how many transitions are made over the course of many trajectories).

The Voelz lab has been working on using MSMs to understand how small changes to a protein, like a single-point mutation or chemical modification, perturb the transition rates. Not surprisingly, perturbations affect some states more than others. It turns out that a particular statistical metric, called the surprisal, can be used to identify the states most affected by perturbations. Using this metric, we can reveal the mechanisms by which perturbations affect dynamics; in the future, this may help us better understand the role of disease-causing mutations. We can also use the surprisal metric to choose states on which to focus more simulations, to help us efficiently interrogate the consequences of different chemical modifications. In this way, we hope to be able to use molecular simulation to help design drugs that mimic stable protein folds. The work is described in a new article published in the Journal of Chemical Theory and Computation (http://dx.doi.org/10.1021/ct500827g).

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iancook221188, Nov 25, 2014

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iancook221188 Ancient Guru

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A subreddit for Folding@home donors to discuss topics
December 3, 2014 by Vijay Pande ·

At https://www.reddit.com/r/foldingathome, we’ve created a subreddit dedicated to improving the bi-directional flow of communication between Folding@home donors, researchers, and developers. Although the official community-driven technical support forum is over in foldingforum.org, that board’s phpbb format makes it challenging for researchers and developers to quickly see what feedback topics are the most popular at a given time. Reddit has several advantages in this regard; it’s easy to upvote topics that are on-topic and helpful, and comments-on-comments feature allows for subtopics to exist without completely derailing the top-level responses.

In short, it’s a better system for certain types of communication than the forum. Although technical support is in the Folding Forum, you can submit topics on the subreddit for general discussions on Folding@home.
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iancook221188, Dec 3, 2014

#273
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IP address for foldingforum.org changing Friday, 12/5
December 3, 2014 by Mark Piercy ·

A quick heads up for Folding Forum users-

SiteGround, who hosts foldingforum.org will be changing the IPs of their cloud servers this Friday, December 5. The change is required in order to ensure better network maintenance and availability. The change should be invisible to most foldingforum.org users. If you get a “Not Found (404)” error message when trying to view the site, try emptying your browser’s cache or flush your computer’s DNS cache and foldingforum.org should show up.
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iancook221188, Dec 3, 2014

#274
iancook221188 Ancient Guru

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Why is the new Folding@home streaming infrastructure (FSI) such a big deal?
December 9, 2014 by Mark Piercy ·

One major benefit of the new Folding@home streaming infrastructure (FSI) over the previous FAH “classic” infrastructure (FCI) is that FSI is streaming. So we get clients running on a trajectory 24×7, whereas FCI has timeouts which can take a while to meet, thus making long trajectories harder to calculate.

Longer trajectories are important to us because Markov State Models (MSMs) need some minimal trajectory length to be useful. The streaming approach gets us there faster and more efficiently (in wall clock time) with fewer wasted Work Units.
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iancook221188, Dec 11, 2014

#275
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Fighting cancer on Folding@home: FDA approved kinase inhibitors
December 26, 2014 by Sonya Hanson ·

You may have noticed a trend in the type of proteins being simulated on Folding@home recently. A number of Folding@home labs are collaborating in an attempt to understand the role of protein conformational heterogeneity (the diversity of structures a protein can readily adopt) in the binding of small molecule drugs that target kinases, proteins that are mutated in a variety of cancers. A number of targeted kinase inhibitors have already been approved by the FDA, and have been shown to significantly improve the lives of patients with breast cancer, as with HER2 inhibitors, chronic myelogenous leukemia, as with Abl inhibitors, and other cancers. We’ve put together an informational poster with the FDA approved small molecule kinase inhibitors. Almost half of these molecules target kinases running on Folding@home: Lapatinib and Afatinib target HER2 (projects 9104-9114); Imatinib, Dasatinib, Ponatinib, Nilotinib, and Bosutinib target Abl (project 10472); Gefitinib, Erlotinib, and Afatinib target EGFR (project 10473); and Dasatinib and Bosutinib also target Src kinase (project 10471). Stay tuned for more blog posts on our progress in this area.

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iancook221188, Dec 27, 2014

#276
iancook221188 Ancient Guru

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Restriction of some GPU projects to pre-maxwell GPUs
January 1, 2015 by Vijay Pande ·

Given some known driver issues with recent NVIDIA maxwell chips and Core18 ( https://www.reddit.com/r/foldingathome/ … l_support/ ), we are temporarily restricting our core18 projects (e.g. 1047*) to use pre-maxwell GPUs. We’ll be making the changes Friday morning. Hopefully this restriction will be a temporary fix, with full maxwell support for FAH in NVIDIA drivers (fixing an OpenCL bug) in the (hopefully near) future.

You can follow this thread in the FCF:

https://foldingforum.org/viewtopic.php?f=74&t=27208
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iancook221188, Jan 2, 2015

#277
iancook221188 Ancient Guru

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Bowman lab update on vision
January 2, 2015 by Greg Bowman ·

Now we have over 1 millisecond of data for rhodopsin, a key signaling protein in vision. In the new year, we will be running more simulations to get better statistics on the behavior of key conformations and delving into the mechanisms of this protein’s conformational changes in response to light.

Happy New Year!
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iancook221188, Jan 2, 2015

#278
iancook221188 Ancient Guru

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New initiative: FAH on Android
January 12, 2015 by Vijay Pande ·

I’m excited to announce today our new initiative for Folding@home on Android Mobile phones, with a beta version being released today. In collaboration with Sony, we have brought Folding@home to Sony Mobile phones starting today with broader Android support in the coming months. The rationale for moving FAH to mobile phones is simple: there are millions of phones and they are becoming extremely powerful. Indeed, with our open source OpenMM code (http://openmm.org) optimized for mobile phones, we get performance comparable to what we were getting on desktops just a few years ago. Moreover, we have completely rewritten our server backend in order to handle the needs of mobile devices. In particular, our Streaming Backend (also known by its internal project name ‘ocore’) can seamlessly distribute work from one phone to another, so even a short amount of compute time on a phone can make an immediate contribution to our project.

With the computer power available, we plan on tackling two key challenges. First out the door is a project on breast cancer. In this project, we are investigating the nature of drug resistance mutations in key proteins (kinases) that are targets for breast cancer drugs. By studying the nature of how these mutations change these key drug targets, we will be able to both advance our basic biophysical understanding of these key proteins as well as build a tool to be used for patient specific breast cancer treatment –– by sequencing the tumor and seeing what mutations are present, our tool seeks to recommend the best drug for a specific patient. Next, we plan to follow this project with a protein folding project, related to misfolding disease (eg Alzheimer’s Disease).

Note that this is a first beta release and certain elements are not in place just yet. Nevertheless, we’re very excited about this next step forward, both that we’re moving into a new space but also that we’ve put the pieces in place such that mobile can make a significant contribution. We have other projects going on as well, so look for other announcements in 2015 for additional FAH initiatives.
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iancook221188, Jan 12, 2015

#279
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New psummary page
January 14, 2015 by Vijay Pande ·

As part of our recent assignment server upgrades we are rolling out a new psummary page (which lists all of the active Folding@home projects). This new page includes projects which are no longer visible in the old psummary system. The new psummary uses a more modern HTML but is otherwise the same.

We have aimed to make psummary backwards compatible with 3rd party tools which parse this data. However, there may be some inconsistencies depending on how these tools operate. To help eliminate such problems in the future we have exposed psummary in JSON format via the AS here:

http://assign.stanford.edu/api/project/summary

http://assign2.stanford.edu/api/project/summary

The new psummary is here:

http://fah-web.stanford.edu/new/psummary.html

The previous HTML psummary will continue to be found here for a while:

http://fah-web.stanford.edu/psummary.html

Note , we plan to eventually deprecate the old psummary and therefore encourage 3rd party tool creators to update their software to use the new URL as soon as possible.
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iancook221188, Jan 16, 2015

#280

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