Vrunda Sheth

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.

Library of Congress Subject Headings

Proteins--Structure--Data processing; Proteins--Structure--Mathematical models; Structural bioinformatics

Publication Date

10-1-2009

Document Type

Thesis

Department, Program, or Center

Thomas H. Gosnell School of Life Sciences (COS)

Advisor

Reyes, Vicente

Comments

Note: imported from RIT’s Digital Media Library running on DSpace to RIT Scholar Works. Physical copy available through RIT's The Wallace Library at: QP551 .S44 2009

Campus

RIT – Main Campus

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