CS234 - Computational Methods for Biomolecular Data



  • Successful output of rotating 3D protein using Java3D
    • Red Spheres: Atoms found in Alpha-Helices
    • Blue Spheres: Atoms found in Beta-Sheets
    • White Spheres: Atoms not found in Alpha-Helices or Beta-Sheets
    • Gray Lines: Connectors show atom adjacency in protein sequence
Unfortunately, it does not appear that Java applets allow input from files on a web-server. Thus, it is not possible to embed the 3D-model into this web page; however, the following three images are screen captures from the specified test proteins:

2BOP (PDB File)
Image of 2BOP protein

1RNB (PDB File)
Image of 1RNB protein

1CD8 (PDB File)
Image of 1CD8 protein



I have selected project 13:

Project 13 Description: PDB viewer. Design a program that parses a PDB file (from the PDB database), and draws a simple picture of the protein using small disks to represent atoms and joining consecutive atoms by lines. Color atoms contained in alpha-helices red, and atoms contained in beta-sheet blue, an other black. Run the viewer on 2BOP, 1RNB, 1CD8 and other two proteins that you may find interesting (courtesy of Daniel Huson).

I plan on using Java to implement this project. My general plan is described below:
  • Discover the specific meaning of each data element (and which elements are useful for this project) in a PDB file
  • Write PDB file-input parser
  • Research the Java extension Java 3D and learn how to model graphics in 3D
  • Model a 3D protein, as specified in the project description, using Java 3D


I have narrowed down the projects I would like to do to the following three projects:

  • 6.) Gene expression analysis.
  • 10.) Benchmarking Gene recognition softwares
  • 13.) PDB viewer
I plan on doing some additonal reserach on these projects before selecting one in the next day or two.