p11706 and p11707 moving to FAH

[rafwiewiora]

11706:
Here we are simulating the NSD2 protein methyltransferase, a continuation of the Chodera Lab effort to map the conformational landscapes of all protein lysine methyltransferases - important epigenetic enzymes. This will provide powerful data for validations of existing chemical probes and inhibitors of this protein class, as well as will facilitate new explorations of the chemical space for further drug candidates.

NSD2's mutations and chromosomal translocations are implicated in reorganizing the epigenetic landscape in cancers such as multiple myelomas and pediatric acute lymphoblastic leukemia. [doi:10.1016/j.molcel.2011.08.042; doi:10.1038/ng.2777; doi:/10.1371/journal.pgen.1004566].

On interesting things about the simulation - we're continuing using the 4-dummy atom zinc atom model [http://www.mayo.edu/research/labs/compu ... a-approach] to model structural zinc clusters in these proteins.

Stats:
# atoms: 62560
credit: 21503
k-factor: 0.75
timeout: 7d
deadline: 10d

Mixed precision calculations are enforced (DP for motion integrations, SP for force calculations). All GPUs lacking DP support are excluded.

11707:
Stats:
# atoms: 35200
credit: 15965
k-factor: 0.75
timeout: 7d
deadline: 10d

11707: Protein lysine methyltransferase SETD8, we have used Ensembler (http://ensembler.readthedocs.org/en/latest/) to generate models from all chains in all available crystal structures - 23 in total. This is the same protein as project 10478, where we started only from two conformations. While I’m analyzing the 1ms (very nice!) of data we’ve gathered there, we’re starting this also with more heterogenous initial conformation seeding. This is part of a bigger ‘operation SETD8’ - next project coming will be a study of this protein in all states of its catalytic cycle to understand changes it undergoes during enzymatic activity and binding of other species.

We have 23 RUNs here, mixed precision is enforced (no-DP GPUs excluded).

Happy Folding! Thanks!

[rafwiewiora]

Project 11707 has just had two new runs added - we're up to 25 RUNs, the new ones are RUN23 and RUN24. These were INTERNAL and BETA tested as project 11709. Please report any potential problems with those two new RUNs, thanks!

[rafwiewiora]

Project 11707 update: to increase the number of jobs available and increase sampling from particular initial configurations, I've made copies of RUN22 - RUN25,26,27,28; RUN23 - RUN29; RUN24 - RUN30. We have 31 RUNs total now then.

[rafwiewiora]

Project 11707 update: many RUNs have been added to increase sampling of some conformations + from newly available crystal structures. We are now at 135 RUNs total (RUN0 - RUN134).