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Tenth anniversary of the first Einstein@Home discovery
Ten years ago, Einstein@Home published its first astronomical discovery. The radio pulsar J2007+2722 was found in July 2010 with our radio pulsar search, analyzing data from the Arecibo Radio Telescope. The discovery [Link] appeared in print on 10 September 2010. A [Link] more detailed article about the discovery was published later.[Link] read more
New paper: Small Molecule Modulation of Intrinsically Disordered Proteins Using Molecular Dynamics Simulations.
Another great GPUGRID-based work: studying the possible modulation of intrinsically disordered proteins through drugs.
Herrera-Nieto P, Pérez A, De Fabritiis G, Small Molecule Modulation of Intrinsically Disordered Proteins Using Molecular Dynamics Simulations. Journal of chemical information and modeling 2020. doi:10.1021/acs.jcim.0c00381
The corresponding badge is labeled "Herrera-Nieto, JCIM 2020".
The extreme dynamic behavior of intrinsically disordered proteins hinders the development of drug-like compounds capable of modulating them. There are several examples of small molecules that specifically interact with disordered peptides. However, their mechanisms of action are still not well understood. Here, we use extensive molecular dynamics simulations combined with adaptive sampling algorithms to perform free ligand binding studies in the context of intrinsically disordered proteins. We tested this approach in the system composed by the D2 sub-domain of the disordered protein p27 and the small molecule SJ403. The results show several protein–ligand bound states characterized by the establishment of a loosely oriented interaction mediated by a limited number of contacts between the ligand and critical residues of p27. Finally, protein conformations in the bound state are likely to be explored by the isolated protein too, therefore supporting a model where the addition of the small molecule restricts the available conformational space.
BOINC database downtime
The LHC@home database will be down for a while this morning, due to a network interruption in the CERN data centre. Hence scheduler requests and uploads will fail for a while.
Sorry for the trouble and happy crunching.
Two new apps launched
Two new apps have been launched, lasievee_small and lasievef_small. As the numbers we factor become larger, the lasieved app has largely become inadequate while the lasievee app queue has grown very long. In an attempt to compensate, job memory use and runtime has crept upward to stretch the capability of the apps. To alleviate these issues, these new apps will provide additional flexibility to choose the app most appropriate to the size of the number being factored while keeping memory use and runtime more reasonable. If you have modified your project preferences to run only specific applications, you may want to adjust your settings to enable these new apps. Thanks for your contributions to NFS@Home!
2020 BOINC Workshop - Call for Volunteers
In light of the cancelation of the 2020 BOINC Workshop in Marburg, Germany, there will be a virtual celebration of BOINC projects, development, and community. As with all things BOINC, your help -- the BOINC community -- is needed to produce the event. Learn more below and at [Link] http://www.boincworkshop.org/.
New paper: Computational and experimental characterization of NF023, a candidate anticancer compound inhibiting…
Here we studied a possible mode of action of NF023, a molecule which disrupts some protein-protein interactions (cIAP-TRAF) misregulated in cancer. The molecule is very charged and flexible, so classical docking studies aren't up to a full modeling... but large-scale MD powered by GPUGRID is.
Cossu F, Sorrentino L, Fagnani E, Zaffaroni M, Milani M, Giorgino T, Mastrangelo E. Computational and experimental characterization of NF023, a candidate anticancer compound inhibiting cIAP2/TRAF2 assembly. J Chem Inf Model. 2020 Aug 21 [Link] doi:10.1021/acs.jcim.0c00518
Protein-protein interactions are the basis of many important physiological processes, and are currently promising, yet difficult, targets for drug discovery. In this context, inhibitors of apoptosis (IAPs)-mediated interactions are pivotal for cancer cell survival; the interaction of the BIR1 domain of cIAP2 with TRAF2 was shown to lead the recruitment of cIAPs to the TNF-receptor, promoting the activation of NF-κB survival pathway. In this work, using a combined in silico-in vitro approach we identified a drug-like molecule, NF023, able to disrupt cIAP2 interaction with TRAF2. We demonstrated in vitro its ability to interfere with the assembly of the cIAP2-BIR1/TRAF2 complex and performed a thorough characterization of the compound’s mode of action through 248 parallel unbiased molecular dynamics simulations of 300 ns (totaling almost 75 µs of all-atom sampling), which identified multiple binding modes to the BIR1 domain of cIAP2 via cl...
New paper: Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p53 using millisecond molecular dynamics simulations
The latest scientific publication obtained with your support and computation is here:
Herrera-Nieto, P., Pérez, A. & De Fabritiis, G. Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p53 using millisecond molecular dynamics simulations. [Link] Sci Rep 10, 12402 (2020).
It investigates an open and difficult problem in biology, namely the structure-function relationship of intrinsically disordered proteins (IDP). IDP proteins are involved in many regulatory processes, and yet are difficult to study both experimentally and computationally. The amount of power provided by GPUGRID volunteers came to the rescue, enabling very extensive sampling of p53, an exemplary IDP involved in oncogenic processes.
The exploration of intrinsically disordered proteins in isolation is a crucial step to understand their complex dynamical behavior. In particular, the emergence of partially ordered states has not been explored in depth. The experimental characterization of such partially ordered states remains elusive due to their transient nature. Molecular dynamics mitigates this limitation thanks to its capability to explore biologically relevant timescales while retaining atomistic resolution. Here, millisecond unbiased molecular dynamics simulations were performed in the exemplar N-terminal region of p53. In combination with state-of-the-art Markov state models, simulations revealed the existence of several partially ordered states accounting for ∼ 40% of the ...
Continued NBody Runs (07/29/2020)
The last set of NBody runs have just converged beautifully. We are currently working on writing the paper to publish these results. In the meantime, we will be replacing these runs with another set:
Thank you all so much for your support. We would not be able to write this paper without your continued assistance.
Enhancing ECM range
I'm enhancing the ecm search range for B1=43e6 up to 2000 digits. Some test workunits are already send out with the name ecm_es_*test* and a short deadline of 1 day. Together with this the credit formula was changed.
New Runs for MilkyWay@home Nbody Simulations (07/29/2020)
I just wanted to let everyone know that new Nbody runs have been put up on MW@home. The last set of runs started converging nicely, so we are confident this next set of runs will converge as well. The names of these runs are:
Please let us know if you have any trouble with these runs. Thank you all for your continued support.