Bioinformatics BI_W0004

Title : Characterization of Local Protein Structure Geometry from the Protein Data Bank-A Senior Project in Bioinformatics
Author : F Lewitter, B Head
Year : 2003
Place of publish : CAHSI 2009 ANNUAL MEETING, 2009
Abstract :

This paper describes the teamed work in a senior
project that involves research in bioinformatics at the
department of computer science. In order to understand
the 3-dimensional (3D) structure of proteins,
specialized database servers are often needed for
specific research questions being studied. In this work,
we are interested in the local structure information
from the Protein Data Bank (PDB). One way to
represent the local structure information is to use the
virtual bond angle and virtual dihedral angle of the
local structure [1]. We have developed a web server to
study the virtual bond angles and virtual dihedral
angles for a selected dataset of 3000 proteins extracted
from the PDB. The web server has improved the
previous server by providing easy access of the
statistical information and the 3D graphics rendering
of the molecule. In particular, the server incorporated a
dynamic graph component and the JMOL molecular
viewer [2] to allow further visualization of the local
geometry. This project was designed for the graduating
seniors consisting of a practical software development
question for which the students explored and developed
a way to build a web server assembled using a MySQL
database, the PHP, Javascript, JavaFx, and graphics
applets such as JMOL.