PDBMine discovers existing protein structures with a similar k-mer sequence of the protein; this structural similarity helps construct its fragmented structure. PDBMine returns torsion angles, which our website clusters and displays in a scatter plot. Furthermore, PDBMine - Data can use these angles to generate a pdb file modeling the potential structure of the protein.
A web application built with Python, Django, Vue.js.
Our objective is to provide efficient computational solutions to better analyze genomic data, i.e., protein structure predictions based on torsion angles (phi-φ and psi-ψ)of previously classified proteins from the Protein Data Bank (PDB) to model a given/unknown amino acid sequence considering a rolling window size (k-mer). K-mer, where k is a given number of amino acid fragments of the user’s interest.
Claire Sturgill, Jenna Pehowski, Timothy Hooks, Naga Venkata Sai Jagjit Satti, Niharika Pandala.
Dr. Homay Valafar, CSE Dept.