NCSI: Supervised Molecular Dynamics for Probing Ligand-protein Interactions p450

Status	Completed
Mentor Name	Edward Ackad
Mentor's XSEDE Affiliation	Startup Allocation
Mentor Has Been in XSEDE Community	4-5 years
Project Title	Supervised Molecular Dynamics for Probing Ligand-protein Interactions p450
Summary	One site on p450 3A4 has been shown to be a periphery site and may also be an allosteric site. This work will used supervised MD to probe what other site are periphery sites, leading to the testing if they are also allosteric sites.
Job Description	The student will run the supervised MD and find the optimal parameters for probing the surface of the protein. They will work on a statistical metric to quantify the binding of the ligand to different protein locations.
Computational Resources	Bridges gpu 100+ SU of supervised MD runs.
Contribution to Community	Our work will continue to show the value in computational biophysics and how it can ask and answer scientific questions not yet possible experimentally. This will allow the community to continue showing that its roll in the Biology Century is pivotal and that clever techniques (such as SuMD) can leverage current hardware to obtain results at timescales not possible for another 5-10 years with standard techniques (conventional MD).
Position Type	Apprentice
Training Plan	The student will familiarize themselves with slurm and named runs as well as the SuMD parameters in the first three weeks. One the runs are started the student will familiarize themselves with jupyter-notebooks and begin theoretical work on a ligand-protein interaction statistical metric.
Student Prerequisites/Conditions/Qualifications	Intermediate experience with any programming language and Linux.
Duration	Summer
Start Date	05/16/2021
End Date	08/15/2021