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1)
Message boards :
News :
Noelia's PhD defence and departure
(Message 43026)
Posted 2962 days ago by noelia Dear all, I have defended my doctoral thesis very recently, on March 4th, and it would have been impossible without your support. My thesis focused on the understanding of ligand-receptor interactions on a different set of systems, in all cases by running simulations in GPUGRID. The thesis itself will be publicly available after an embargo period (here is the link in any case: http://hdl.handle.net/10803/363212) due to the still-unpublished works it contains. In summary, with the support of GPUGRID we have produced works on seven systems, three are already published, two under review and the two left will be submitted very soon (so expect new badges soon!!). I must also say that I will be no longer working in GPUGRID. I have already moved to Boston where I will apply the methods that I have learned working on here to drug discovery programs. Many thanks again, Noelia |
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2)
Message boards :
News :
Badges ready for the last paper!
(Message 42404)
Posted 3053 days ago by noelia Hello guys! We recently published a paper which used a considerable amount of GPUgrid simulations. It would not have been possible without your contributions. The paper is: N. Ferruz, M. J. Harvey, J. Mestres and G. De Fabritiis, Insights from Fragment Hit Binding Assays by Molecular Simulations, J. Chem. Inf. Model., 2015, 55, pp 2200-2205 You can also browse ranking positions ;) : https://www.gpugrid.net/science.php?topic=methods Thanks to all! Noelia |
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3)
Message boards :
Number crunching :
NOELIA Error
(Message 42159)
Posted 3086 days ago by noelia Hi KSUMatt, Sorry to hear your about your error. Just tried in a local machine and worked fine, we're having a look at it. Please report if this error pops again. Thanks for your time! Noelia |
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4)
Message boards :
Number crunching :
Short runs
(Message 41250)
Posted 3248 days ago by noelia Hi Speedy, This short tasks are based in the Dopamine 3 receptor. It is a target for treating schizophrenia, Parkinson's, drug abuse and other neurological disorders. This receptor is involved in many complex pathways in the central nervous system and its dysfunction affects in a variety of neuropsychiatric disorders which are not yet well understood. With this experiments, we are trying to understand how eticlopride (ETQ) interacts with it and exerts its action. This molecule is known to bind and block the receptor, and therefore it is mainly used for the schizophrenia treatment. It's mechanism of binding, although would be very interesting for the design of other similar molecules, it is yet not known and that's what we are trying to understand with this simulations. Many thanks for your time! |
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5)
Message boards :
News :
WU: THROMBIN
(Message 37133)
Posted 3594 days ago by noelia Hi guys, There was a bug for some unexpected reason in this batch and we apologize. As you were having problems validating i've cancelled those WUs that still were unsent and resend them -THROMBIN1-. Those which were running can still be completed and you won't lose any credit. Theoretically minimum quorum should be now 1, but please report if you notice any problem. Noelia |
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6)
Message boards :
News :
WU: THROMBIN
(Message 37079)
Posted 3598 days ago by noelia Hi guys!! There's a new project in the long queue ( NOELIA_THROMBIN ) . It consists of the binding of 6 different inhibitors to the protease thrombin, a protein in the coagulation cascade. With these, we are trying to demonstrate that molecular simulations can be as useful as X-Ray crystallography predicting binding modes. Thanks to all, P.D: Report any problems please! Noelia |
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7)
Message boards :
News :
WU: TRPS1S4
(Message 37042)
Posted 3606 days ago by noelia Hi Jeremy, Yes, there was a problem in the configuration file of those batches - which made they had no charm in windows indeed! - I tested the WUs in a linux workstation so didn't notice any issues. Stopped and fixed those ones and all the series TRPXXX and SH2XX should not have any problem now. Thanks! |
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8)
Message boards :
News :
WU: TRPS1S4
(Message 37036)
Posted 3606 days ago by noelia Dear all, Just sent 1000 WUs under the group name TRPS1S4. This is probably the last batch of a project you've been crunching for more than one year now (WUs: FXA, FXArep.. and similar names) for thrombosis disease. This last batch is particularly important, since will allow us to see if these simulations can predict experimental outcomes. Please report any problems. Thanks to all and happy crunching! Noelia |
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9)
Message boards :
News :
WU: BI_3
(Message 36866)
Posted 3630 days ago by noelia Hi all! Just sent a new project to the long queue, around 2500WUs, ~100,000 credits each. In particular, this project will help us to understand how antidiabetic drugs block its target, but also to develop a better general method for other targets and drugs involved in different diseases. Thanks to all!! |
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10)
Message boards :
News :
WU: FXArep
(Message 34601)
Posted 3761 days ago by noelia We realized we needed one last bunch of WUs to finish the project. We've already started writing, so should be able to post final results sometime soon, hopefully :) thanks!! |
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