PrimeGrid - International Women's Day Challenge on March 8th
Détails
Welcome back from Tour de Primes! We're kicking off March with a lightning round single-day challenge! Read on...
The second challenge of the 2023 Series will be on International Women's Day, a global holiday celebrated annually on March 8 as a focal point in the women's rights movement, bringing attention to issues such as gender equality, reproductive rights, and violence and abuse against women. The challenge will be 1-day in duration and offered on the SGS-LLR application, beginning 08 March 15:00 UTC and ending 09 March 15:00 UTC.
To participate in the Challenge, please select only the Sophie Germain Prime Search (LLR) project in your PrimeGrid preferences section.
Nonplussed? Nostalgic? Nihilistic? Nervous? Newly inspired? Join the discussion at https://www.primegrid.com/forum_thread.php?id=10168
The M Queens subproject has finished last weekend. No more workunits are distributed. Now we are analyzing the results which are 8 GB of compressed data. Much thanks for your provided work.
Hello GPUGRID!
You‘ve already noticed that a new app called “ATM†has been deployed with some test runs. We are working on its validation and deployment, so expect more jobs to come on this app soon. Let me briefly explain what this new app is about.
The ATM application
The new ATM application stands for Alchemical Transfer Method, a methodology Emilio Gallicchio et al. designed for absolute and relative binding affinity predictions. The ATM method allows us to estimate binding affinities for molecules against a specific protein, measuring the strength at which they bind. This methodology falls under the category of alchemical free energy calculation methods, where unphysical intermediate states are used to estimate the free energy of physical processes (such as protein-ligand binding). The benefits of ATM, when compared with other common free energy prediction methods (like the popular FEP), come from its simplicity, as it can be used with any forcefield and does not require a lot of expertise to make it work properly.
Measuring experimental binding affinities between candidate molecules and the targeted protein is one of the first steps in drug discovery projects, but synthesizing molecules and performing experiments is expensive. Having the capacity to perform computational binding affinity predictions, particularly during drug lead optimization, is extremely beneficial. We are actively working now on testing and validating the ATM method so that we can start applying it to real drug discovery projects as soon as possible. Additionally, since these methods are usually applied to hundreds of molecules, it benefits a lot from the parallelization capabilities of GPUGRID, so if everything goes as expected, this could potentially send lots of work units.
The ATM app is based on Python, similar to the PythonRL application, where we ship it with a specific python environment.
Here are the two main references for the ATM method, for both absolute and relative binding affinity predictions:
Absolute binding free energy estimation with ATM: https://arxiv.org/pdf/2101.07894.pdf
Relative binding free energy estimation with ATM:
https://pubs.acs.org/doi/10.1021/acs.jcim.1c01129
For now we are only able to send jobs to Linux machines but we are hoping to have a Windows version soon.
As all of you already know we are constantly struggling with our problematic storage. The University have bought a new one and they planned the moving procedure. The HPC cluster should be moved this Monday (March, 6th), the other resources will follow.
I will reasonably shut down the server when needed, I will tell you when as soon as I know the date. Meanwhile the work generator will be active just a few hours a day, so very few workunits will be available.
Thank you all for your understanding and patience.
