CS234 - Computational Methods for Biomolecular Data
2/15/2010
Progress:
- 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
2BOP (PDB File)
1RNB (PDB File)
1CD8 (PDB File)
2/12/2010
Progress:
- Successful input of PDB file (ATOMs and HETATMs)
- Stores all relevant data as specified in the Atomic Coordinate Entry Format Description, V_3.2
2/1/2010
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
1/31/2010
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