p11706 and p11707 moving to FAH
Posted: Tue May 03, 2016 6:33 pm
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!
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!