Visualization of protein 3D structures in reduced representation with simultaneous display of intra and inter-molecular interactions

Show full item record

Title: Visualization of protein 3D structures in reduced representation with simultaneous display of intra and inter-molecular interactions
Author: Sheth, Vrunda
Abstract: Protein structure representation is an important tool in structural biology. There exists different methods of representing the protein 3D structures and different biologists favor different methods based on the information they require. Currently there is no available method of protein 3D structure representation which captures enough chemical information from the protein sequence and clearly shows the intra-molecular and the inter-molecular H-bonds and VDW interactions at the same time. This project aims to reduce the 3D structure of a protein and display the reduced representation along with inter-molecular and the intra-molecular H-bonds and van der Waals interactions. A reduced protein representation has a significantly lower "atomicity" (i.e., number of the coordinates) than one which is in all-atom representation. In this work, we transform the protein structure from 'all- atom representation' (AAR) to 'double-centroid reduced representation' (DCRR), which contains amino acid backbone (N, C[alpha], C', O) and side chain (C[beta] and beyond) centroid coordinates instead of atomic coordinates. Another aim of this project is to develop a visualization interface for the reduced representation. This interface is implemented in MATLAB and displays the protein in DCRR along with its inter-molecular, as well as intra-molecular, interaction. Visually, DCRR is easier to comprehend than AAR. We also developed a Web Server called the Protein DCRR Web Server wherein users can enter the PDB id or upload a modeled protein and get the DCRR of that protein. The back end to the Web Server is a database which has the reduced representation for all the x-ray crystallographic structure in the PDB.
Record URI: http://hdl.handle.net/1850/10857
Date: 2009-10

Files in this item

Files Size Format View
31870_pdf_28276 ... 11DE-A0FC-860C3012225A.pdf 1.623Mb PDF View/Open

The following license files are associated with this item:

This item appears in the following Collection(s)

Show full item record

Search RIT DML


Advanced Search

Browse