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 metalated form at a molecular level by running molecular dynamics simulations using NAMD.
Job Description	Student will create XSEDE account, use computational resource from research allocation for the project Investigation of Metal Binding in Psoriasin using Molecular Dynamics Simulations to run molecular dynamics (MD) simulation using NAMD.The student willlearn to manage and store data using XSEDE resources. They will also use VMD for visualization and analysis of data followed by plotting the analyzed data using python and matplotlib.
Computational Resources	The project will use XSEDE research allocation for the project 'Investigation of Metal Binding in Psoriasin using Molecular Dynamics Simulations' (BIO210014).
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	Learner
Training Plan	1) Linux - The student would create and use their XSEDE account through terminal using resources like putty to access and navigate bridges-2 resources. 2) MD simulation- The student will learn to run molecular dynamics simulation using the NAMD software. They would also learn to manage and store the collected data using XSEDE resources. 3) VMD- The student will learn to use VMD for visualizing protein and simulation trajectories followed by performing data analysis using tcl script and rendering images. 4)Data analysis and visualization- The student will learn to plot analyzed data using tools like python/matplotlib and create publication quality images from their data
Student Prerequisites/Conditions/Qualifications	The student is required to have a background in chemistry and biochemistry to understand the basics of molecular structure and structure-function relationship in proteins.
Duration	Quarter
Start Date	08/30/2021
End Date	11/30/2021