Projects 17505-17507 (GPU, OpenMM Core22) to FAH

[jiayeguo]

Projects 17505-17507 are now in FAH.

STATS:
17505:
<atoms v=“50252”/>
<timeout v=“2.0”/>
<deadline v=“3.0”/>
<stats-credit v=“10974”/>

17506:
<atoms v=“50046”/>
<timeout v=“2.0”/>
<deadline v=“3.0”/>
<stats-credit v=“10707”/>

17507:
<atoms v=“50047”/>
<timeout v=“2.0”/>
<deadline v=“3.0”/>
<stats-credit v=“10092”/>

GPU constraints for all three projects:
[GPU=NVIDIA GPUSpecies<6]
GPU!=AMD
(Cause=CANCER Cause=ANY)

The goal of this set of experiments is to explore the mechanism of the complex between N-MYC (an oncoprotein) and AURKA (a kinase that’s important in many cancers) being destabilized by certain small-molecule AURKA inhibitors. Project 17505 is room-temperature vanilla simulation of apo AURKA : N-MYC complex to explore protein-protein interactions without small molecule binding. Projects 17506 and 17507 are room-temperature vanilla simulations of AURKA : N-MYC complex with two different small-molecule inhibitors bound to explore protein-protein interactions under the effect of these inhibitors. Once we have better ideas of the protein-protein interaction patterns, we also hope to eventually build some Markov State Models of these systems to quantify the different conformational states. Thanks in advance!