1) Message boards : News : New badges! (Message 44796)
Posted 2 days ago by Toni
Dear all!

We added badges for two great papers which came out this year. Both appeared in Scientific Reports, a highly-regarded open-access journal.

I don't think I can do better justice to the works than the author's own words, so I am copying here their abstracts, which hopefully convey the gist of the respective impact:

  1. Noelia's study of ions binding to the myo-inositol monophosphatase enzyme:

    Molecular recognition is rarely a two-body protein-ligand problem, as it often involves the dynamic interplay of multiple molecules that together control the binding process. Myo-inositol monophosphatase (IMPase), a drug target for bipolar disorder, depends on 3 Mg2+ ions as cofactor for its catalytic activity. Although the crystallographic pose of the pre-catalytic complex is well characterized, the binding process by which substrate, cofactor and protein cooperate is essentially unknown. Here, we have characterized cofactor and substrate cooperative binding by means of large-scale molecular dynamics. Our study showed the first and second Mg2+ ions identify the binding pocket with fast kinetics whereas the third ion presents a much higher energy barrier. Substrate binding can occur in cooperation with cofactor, or alone to a binary or ternary cofactor-IMPase complex, although the last scenario occurs several orders of magnitude faster. Our atomic description of the three-body mechanism offers a particularly challenging example of pathway reconstruction, and may prove particularly useful in realistic contexts where water, ions, cofactors or other entities cooperate and modulate the binding process.

  2. Nathan's study of S1PR1 receptor:

    The binding process through the membrane bilayer of lipid-like ligands to a protein target is an important but poorly explored recognition process at the atomic level. In this work we succeeded in resolving the binding of the lipid inhibitor ML056 to the sphingosine-1-phosphate receptor 1 (S1P1R) using unbiased molecular dynamics simulations with an aggregate sampling of over 800 μs. The binding pathway is a multi-stage process consisting of the ligand diffusing in the bilayer leaflet to contact a “membrane vestibule” at the top of TM 7, subsequently moving from this lipid-facing vestibule to the orthosteric binding cavity through a channel formed by TMs 1 and 7 and the N-terminal of the receptor. Unfolding of the N-terminal alpha-helix increases the volume of the channel upon ligand entry, helping to reach the crystallographic pose that also corresponds to the predicted favorable pose. The relaxation timescales of the binding process show that the binding of the ligand to the “membrane vestibule” is the rate-limiting step in the multi microseconds timescale. We comment on the significance and parallels of the binding process in the context of other binding studies.

Edit: The Science page does not contain the new papars yet, but you will find them in your profile page. WU names were respectively like 1mgx1, 1mgx2, 3mgx1, 3mgx2, 5MG, 20MG, 20MG2, INSP, INS1P (Noelia's) and RPS1 (Nate's).

2) Message boards : News : Disk full (solved) (Message 44620)
Posted 18 days ago by Toni
Thanks. Possibly fixed.
3) Message boards : News : Disk full (solved) (Message 44618)
Posted 18 days ago by Toni
...aaand should be solved.
4) Message boards : News : Disk full (solved) (Message 44617)
Posted 18 days ago by Toni
One of the disks of the server is full, and the project is down. Apologizes for the problem! We are trying to fix it.

5) Message boards : GPUGRID CAFE : Sony OtherOS refund (Message 43827)
Posted 120 days ago by Toni
For those still around from the PS3 times... :)

6) Message boards : News : Server performance (Message 40346)
Posted 598 days ago by Toni
Did the corresponding page in other projects also slow down? May be due to slower responses from external servers handling the CPID (namely boinc.netsoft-online.com).
7) Message boards : Graphics cards (GPUs) : AMD openCL work??? (Message 39749)
Posted 634 days ago by Toni
See here
. :)
8) Message boards : News : WARNING/CHALLENGE: VERY LONG WU (VERYLONG_CXCL12_confAna) (Message 39660)
Posted 638 days ago by Toni
I've raised the limit in the DB for VERYLONG WUs. I'm not sure whether such changes propagate to clients at some time.
9) Message boards : Server and website : Upload Problems (Message 37654)
Posted 796 days ago by Toni
An update: we have been freeing up space since Sunday night. The resolution is not instantaneous because:

1. deleting huge amount of files is slow
2. as soon as files are deleted, the freed up space is used by newly uploaded WUs.

So, please don't worry if things take some time to go back to normality.

The increase in required space is partly due to new WU types (e.g. the CPU experiments).

Addition of HD space has been of course considered, but with the current server it is sadly not possible for hardware reasons.
10) Message boards : Server and website : Upload Problems (Message 37646)
Posted 796 days ago by Toni
Believe it or not, dedicated people are working on the overworked server regardless of the time of the day. When the disk is full it takes time even to delete files.

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