Dissertations and Theses @ UNI
Availability
Open Access Thesis
Keywords
Proteins--Conformation; Proteins--Structure--Computer simulation; Academic theses;
Abstract
Proteins play a central role for biological activities and have a fundamental impact in several different research fields such as drug discovery. Nowadays research in structural biology strongly relies on the support of computational power. Computers help to handle the large amounts of data that are instantly increasing. An area where computers are particularly essential is the visualization of protein structures in three-dimensional space. By studying the structure of a protein, further conclusions can be drawn about its function and other proteins that are similar in their conformation. Many software packages have been developed for displaying three-dimensional protein structures. They provide options for visualizing proteins, perform operations for further analysis and sometimes compare two structures to each other. However, there are limited possibilities to include an existing alignment or align protein conformations within the program. This research project describes the software package StructAlign Viewer. It can be used in a standalone mode or in conjunction with the MaxPairs algorithm for optimal protein structure alignment. The software is built on the Java platform. The user interface is based on Java Swing and the 3D visualization area is realized through Java 3D. StructAlign Viewer has the ability to visualize single protein structures by reading out their information from existing PDB files and displaying them in different ways. The software can upload two proteins and an existing alignment file that holds information about their sequence alignment. However, the main purpose of StructAlign Viewer is to visualize the structural alignment of two proteins in real-time. The calculation itself is being processed by the MaxPairs algorithm. StructAlign Viewer provides a graphical user interface, where it is possible to access all available commands. With those features equipped, the software opens new possibilities for the analysis of protein structures and structure comparison.
Year of Submission
2011
Degree Name
Master of Science
Department
Department of Computer Science
First Advisor
Aleksandar Poleksic
Second Advisor
Mark A. Fienup
Third Advisor
Michael H. Walter
Date Original
2011
Object Description
1 PDF file (73 leaves)
Copyright
©2011 Harald Kattnig
Language
en
File Format
application/pdf
Recommended Citation
Kattnig, Harald, "StructAlignViewer: A Software Package for Visualizing Protein Structural Alignments in Real-Time" (2011). Dissertations and Theses @ UNI. 3132.
https://scholarworks.uni.edu/etd/3132
Comments
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