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#33
GPUGRID / Re: Project News - GPUGrid
Last post by Dingo - May 03, 2024, 12:16:15 AMQuote[GPUGrid.net] In-silico Binding Assay (ISBA/ACEMD3)
This is a message Adrià posted in our discord channel. Since he doesn't have an account in the GPUGRID forum I open the thread for him. If you want to be more up to date to the news related to this project and others please join our discord, we are usually more active there: https://discord.gg/dCMkcafPpX
Hello GPUGRID! Here Adrià. I'll be recovering the ACEMD3 application again, and sending new jobs of standard MD simulations (We've been testing it these past weeks to make sure it worked well for both Windows and Linux) The main goal of these new batch of simulations will be to validate further our capacity to predict the binding mode of ligands using simulations and adaptive sampling methods. Those of you that have been around for some time here might already be familiar with these simulations, such as the Benzamidin-Trypsin system (https://www.pnas.org/doi/abs/10.1073/pnas.1103547108) or the Dopamine D3 receptor with an antagonist ligand (https://www.nature.com/articles/s41598-018-19345-7#Ack1), which we were able to simulate thanks to GPUGRID and all your effort! Now, we are revisiting this method, which we call in-silico binding assay (ISBA). During drug discovery campaings, it's common that you know of ligands that bind to your target, but you don't know their binding mode, the exact conformation and structure that both the ligand and the protein have when bound. Knowing the binding mode is critical for further development of the molecule into a potent and usable drug. The most precise way of discovering the binding mode is with crystallization. However, that can take too much time or be directly impossible, depending on the protein. Therefore, we want to optimize and refine ISBA for binding mode prediction, so it can be usable during drug discovery projects. To summarize a bit our objectives, we want to predict binding modes for larger molecules than Benzamidin, with the same precision, but with less simulation time that was needed for the D3 receptor system. To do so, we'll be using the latest version of adaptive sampling that we developed, AdaptiveBandit (https://pubs.acs.org/doi/abs/10.1021/acs.jctc.0c00205). The objective of these new simulations I'll be sending will be to benchmark AdaptiveBandit in an ISBA scenario, improve the algorithm if required and fine-tune its hyperparameters. Let me know if there's any issue with the simulations. I'll be sending 100ns trajectories for the most part, divided in two steps.
View article · Thu, 2 May 2024 09:28:34 +0000
#34
LODA / Re: Is LODA still running?
Last post by jave808 - May 02, 2024, 09:56:42 AM #35
OPEN DISCUSSION / Re: BOINCStats - Willy's Healt...
Last post by jave808 - May 02, 2024, 07:58:41 AMUpdate on Willy's health. He's had an operation and is recovering.
https://www.boincstats.com/forum/1,1/12703,1
https://www.boincstats.com/forum/1,1/12703,1
#36
OPEN DISCUSSION / Re: Humor
Last post by Cruncher Pete - May 01, 2024, 08:55:00 AMBill and Bob, two young guys, were sitting outside a clinic.Bill happened to be crying very loudly."Why are you crying?" Bob asked."I came here for a blood test," sobbed Bill."So? Are you afraid?""No. For the blood test, they cut my finger."As Bob heard this, he immediately began crying profusely.Astonished, Bill stopped his tears and asked Bob,"Why are you crying now?"To which Bob replied,"I came for a urine test!"
#38
OPEN DISCUSSION / Re: Humor
Last post by Cruncher Pete - April 30, 2024, 08:33:48 AMThree swordsmen, a Christian, a Muslim and a Jew were arguing over who was the best, so they decided to have a little contest.First up was the Christian, who took his mighty sword and with two blows he cut a tree in half. Such strength. Such power. Everyone was impressed.Next was the Muslim, who threw a silk handkerchief in the air, and then in one stroke he drew his fine, sharp Damascus blade and cut the handkerchief in half as it fell. Such sharpness, such precision. Everyone congratulated him.Finally it was the Jewish swordsman's turn. He took out a relatively small sword and his competitors looked at him and almost laughed. Then he pulled out a small wooden box, set it on the table, and said, "In here is a fly." He opened the box and as the fly came out and flew away, he slashed at it, once. But the fly just kept on flying. Now the other two swordsmen DID laugh. So he looked at them and said, "What? Doesn't circumcision count?"