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<project type="OPENMM_22" id="18202">
<stats-credit v="67770"/>
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<deadline v="5"/>[GPU] Project 18202 now on FAH (GPU, OpenMM Core22)
Moderators: Site Moderators, FAHC Science Team
[GPU] Project 18202 now on FAH (GPU, OpenMM Core22)
Project 18202 is now on folding at home! We are simulating one of the Alzheimer's associated proteins, apolipoprotein E4 (apoE4) in hopes of better understanding how this isoform contributes to Alzheimer's disease pathology and how we can reverse this pathology.
https://stats.foldingathome.org/project/18202
Re: [GPU] Project 18202 now on FAH (GPU, OpenMM Core22)
Hi all, Apologies as I forgot to update this post last week. Approximately one and a half weeks ago highland1, the work server which this project is housed on, was overloaded and then suffered several performance issues as a result. We temporarily halted jobs last week in attempt to resolve these server issues. We think we finally have a fix for the issues we were seeing (everything is performing well during testing) and we are now slowly opening the project again. If you find that you are having issues returning WUs, being credited points, or anything else please let us know by posting in this forum: viewforum.php?f=19. As always, thank you for folding!
Re: [GPU] Project 18202 now on FAH (GPU, OpenMM Core22)
As a quick update to this project- we've acquired a huge amount of data (around 3.4ms of aggregate simulation time!) and are in the process of analyzing this data now. We may decide to re-release this project in the future if we need further sampling, but for the time being we've paused further issuing of these WU. We are continuing to collect data on other apolipoprotein E isoforms in projects: 18201 (GPU, OpenMM) and 18210 (CPU, A8), in an effort to understand why people with those isoforms are less likely to develop Alzheimer's Disease than people with this isoform of ApoE. Thank you to everyone who's helped out on this project!
Re: [GPU] Project 18202 now on FAH (GPU, OpenMM Core22)
Hi all,
One more note on this project. We've finished a first pass analysis on the data we collected for p18202 and have written a paper detailing this analysis and findings. While this paper is still in peer review for official publication, we've made the paper available via the biology preprinting server, Biorxiv. You may find the paper here: https://www.biorxiv.org/content/10.1101 ... 2.478828v1. (or search Biorxiv Apolipoprotein E4 has extensive conformational heterogeneity in lipid free and bound forms).
Here are the highlights-
This project highlights the strongest genetic risk factor for Alzheimer's disease, ApoE. People with two copies of ApoE4 are ~12-15x more likely to develop Alzheimer's disease than people who have the more common variant, ApoE3. Our hope is that by understanding how ApoE isoforms adopt different conformations, and how those conformations lead to disease, we may be able to develop drugs that change or fix the conformations of bad-acting ApoE variants. While ApoE has been studied for many years, "seeing" ApoE has had a lot of challenges. For the first time, we present ApoE in atomistic detail. We find several interesting findings, including that parts of ApoE are highly dynamic, an underappreciated fact before now. We also find that many other parts of the protein adopt not one, but several stable conformations. We will continue to explore other ApoE variants (p18201 for GPU, 18210 for CPU), as well as explore this dataset in much more depth in future work.
A huge thank you to everyone who has contributed their time and energy to this project.
One more note on this project. We've finished a first pass analysis on the data we collected for p18202 and have written a paper detailing this analysis and findings. While this paper is still in peer review for official publication, we've made the paper available via the biology preprinting server, Biorxiv. You may find the paper here: https://www.biorxiv.org/content/10.1101 ... 2.478828v1. (or search Biorxiv Apolipoprotein E4 has extensive conformational heterogeneity in lipid free and bound forms).
Here are the highlights-
This project highlights the strongest genetic risk factor for Alzheimer's disease, ApoE. People with two copies of ApoE4 are ~12-15x more likely to develop Alzheimer's disease than people who have the more common variant, ApoE3. Our hope is that by understanding how ApoE isoforms adopt different conformations, and how those conformations lead to disease, we may be able to develop drugs that change or fix the conformations of bad-acting ApoE variants. While ApoE has been studied for many years, "seeing" ApoE has had a lot of challenges. For the first time, we present ApoE in atomistic detail. We find several interesting findings, including that parts of ApoE are highly dynamic, an underappreciated fact before now. We also find that many other parts of the protein adopt not one, but several stable conformations. We will continue to explore other ApoE variants (p18201 for GPU, 18210 for CPU), as well as explore this dataset in much more depth in future work.
A huge thank you to everyone who has contributed their time and energy to this project.
Re: [GPU] Project 18202 now on FAH (GPU, OpenMM Core22)
Hi all,
A quick note that we're reopening this project for a little while in order to get more sampling on some of our clones to match our other project (p18201) so we have truly equal comparisons between the datasets. You should start to see (if you haven't already) WUs from Clones 0 + 1 of this project.
Thanks!
A quick note that we're reopening this project for a little while in order to get more sampling on some of our clones to match our other project (p18201) so we have truly equal comparisons between the datasets. You should start to see (if you haven't already) WUs from Clones 0 + 1 of this project.
Thanks!