NCSI: Investigation of Metal Binding in Psoriasin using Molecular Dynamics Simulations

Status	Completed
Mentor Name	Deepika Das
Mentor's XSEDE Affiliation	Research allocation
Mentor Has Been in XSEDE Community	1-2 years
Project Title	Investigation of Metal Binding in Psoriasin using Molecular Dynamics Simulations
Summary	This study aims to understand the structural variations of psoriasin by providing a comparative analysis of the chemical and biophysical properties for the two structures of psoriasin in apo and two different metalated forms (low and high zinc structures) at a molecular level by running molecular dynamics simulations using NAMD.
Job Description	Student will focus on the analyzing the data from running MD simulations as a learner in the EMPOWER program. She will use VMD on supercomputer through terminal to analyze data to calculate quantities like Hbonds, net RMSD, RMSF etc. for large data sets (multiple replicates of several systems), to successfully store and transfre data, plot the results and have contribution in terms of using the collected data to modify/extend the course of the project,
Computational Resources	The project will use XSEDE research allocation for the project 'Investigation of Metal Binding in Psoriasin using Molecular Dynamics Simulations' (BIO210014). The PI will then apply for a renewal.
Contribution to Community	This project will enable exposure of second-year undergraduates to scope of computational resources and pave the development of a large-scale student engagement.This project will also result in a publication with undergraduate stuednts as primary authors.
Position Type	Apprentice
Training Plan	The student has been trained in the bascis of molecular dynamics and running simulation on bridges2 using terminal. The apprentice position will be more focused on data analysis and representation. In particular, she will be working on running VMD on supercomputer through terminal to analyze data to calculate quantities like Hbonds, net RMSD, RMSF etc. for large data sets (multiple replicates of several systems) and to successfully store and transfre data. She will also be learning to plot analyzed data using tools like python/matplotlib/R and create publication quality images from collected data. The next part will be focused on training her to use the obseevables to plan the next step of the study.
Student Prerequisites/Conditions/Qualifications	The student has been working with me as learner in EMPOWER program for the last quarter and has been learning the basics of molecular dynamics and using VMD. She is alos currently taking a course with me that studies the structure-function relationship of proteins.
Duration	Semester
Start Date	01/03/2022
End Date	04/01/2022