Projects 17308-9 (GPU, OpenMM Core22) on Fah
Posted: Tue Oct 20, 2020 1:16 am
Projects 17308-9 now on fah!
Stats:
17308:
<atoms v="158384"/>
<timeout v="2.0"/>
<deadline v="3.0"/>
<stats-credit v="25289"/>
GPU constraints: GPU=NVIDIA GPUSpecies>=6, GPU=AMD GPUSpecies>=5
17309:
<atoms v="200474"/>
<timeout v="2.0"/>
<deadline v="3.0"/>
<stats-credit v="36800"/>
GPU constraints: GPU=NVIDIA GPUSpecies>=6, GPU=AMD GPUSpecies>=5
These projects involve the SARS-CoV-2 receptor binding domain (RBD) and its target receptor in humans, ACE2. We are simulating these proteins alone and in complex with each other (and with and without glycosylation). We will build Markov State Models using the Fah simulation data, which will help us identify the metastable states of each protein/protein complex. Given these experiments, we hope to be able to explain the impact of glycosylation on RBD conformational dynamics as well as identify whether there are shifts in metastable states upon RBD:ACE2 binding. Ultimately, the knowledge gained here will help inform drug design efforts.
For more information: https://stats.foldingathome.org/project?p=17307
Notes:
- Projects 17307-9 are replacing 17304-6 (as announced here: viewtopic.php?f=24&t=36252) due to work server issues
- Project 17307 will require some more testing, so this one will be announced next week
Thanks everyone!
Stats:
17308:
<atoms v="158384"/>
<timeout v="2.0"/>
<deadline v="3.0"/>
<stats-credit v="25289"/>
GPU constraints: GPU=NVIDIA GPUSpecies>=6, GPU=AMD GPUSpecies>=5
17309:
<atoms v="200474"/>
<timeout v="2.0"/>
<deadline v="3.0"/>
<stats-credit v="36800"/>
GPU constraints: GPU=NVIDIA GPUSpecies>=6, GPU=AMD GPUSpecies>=5
These projects involve the SARS-CoV-2 receptor binding domain (RBD) and its target receptor in humans, ACE2. We are simulating these proteins alone and in complex with each other (and with and without glycosylation). We will build Markov State Models using the Fah simulation data, which will help us identify the metastable states of each protein/protein complex. Given these experiments, we hope to be able to explain the impact of glycosylation on RBD conformational dynamics as well as identify whether there are shifts in metastable states upon RBD:ACE2 binding. Ultimately, the knowledge gained here will help inform drug design efforts.
For more information: https://stats.foldingathome.org/project?p=17307
Notes:
- Projects 17307-9 are replacing 17304-6 (as announced here: viewtopic.php?f=24&t=36252) due to work server issues
- Project 17307 will require some more testing, so this one will be announced next week
Thanks everyone!