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Group 7 Capstone Project
Fall 2023
Team: Jovanny Duran Salgado, Durga Narayana Varma Addepalli, DIVYA SRI Ambati, Pooja Venkata Ramana Adapa, and Travis Meeks
Department Presentation
Department Presentation
Mission of the project
Mission of the project
Research and design a database of protein-protein interaction pairs, using Molecular Dynamics (MD) simulations, and VMD protein interaction analysis. The domain topics include SARS-CoV-2 Spike protein interacting with human ACE2 protein.
Big goal: Reveal the mechanisms of the interactions between virus and human proteins
The student team will act as the database designer and engineer. The student team will be given an extensive list of protein-protein complex structures. The student team is tasked to design a database for academic research on virus interactions, including SARS-CoV-2 Spike protein interacting with human ACE2 protein.
Milestone 1
Milestone 1
Investigate existing database to determine whether it’s usable for research on protein-virus interactions
Obtain an understanding of how to use Molecular Dynamics simulations and VMD protein interaction analysis tool
Determine whether existing dataset is useable, and if not, collect a new dataset
Create specifications for potential database (platform, DB type, cloud/on-prem)
Milestone 2
Milestone 2
The team will have database designed for the protein- virus interactions for testing
Performing MD simulations and extracting data from it
Milestone 3
Milestone 3
Test final database to determine whether it is suitable for protein-virus interaction research
Test and validate protein interaction simulation
Project Handoff
Project Handoff
Complete documentation for project hand off to Dr. Chloe Yixin Xie
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