Refactoring the Code for Visualizing Protein Database Information in a 3D Viewer for Software Reusability

  • Chun, Yoo-Jin (Department of Computer Science, Ewha Womans University) ;
  • Ham, Seong-Il (Department of Architectural Engineering, Yonsei University) ;
  • Yang, San-Duk (Department of Computer Science, Ewha Womans University) ;
  • Rhie, Arang (Department of Computer Science, Ewha Womans University) ;
  • Park, Hyun-Seok (Institute of Bioinformatics, Macrogen Inc.)
  • Published : 2008.03.31


We have released five Java Application Programming Interface (API) packages for viewing three-dimensional structures of proteins from the Protein Data Bank. To this end, the user interface of an earlier version has been refactored in an object-oriented fashion, in which refactoring is the process of changing a software system to improve its internal structure, without altering the external behavior. Various GUI design and features have been provided conveniently thanks to the Model-View-Control (MVC) model, which is an architectural pattern used in software engineering. Availability: The source code and API specification can be downloaded from


  1. Cho, M.K., et al. (2007). The AB05 NIAB tools workbench for building automatic biopathway maps for agricultural organisms. G&I. 5, 95-97.
  2. DeLano, W.L. (2002). The PyMOL molecular graphics system. DeLano Scientific. (San Carlos, CA, USA: DeLano Scientific)
  3. Berman, H.M., Battistuz, T., Bhat, T.N., Bluhm, W.F., Bourne, P.E., Burkhardt, K., Feng, Z., Gilliland, G.L., Iype, L., Jain, S., et al. (2002). The protein data bank. Biopolymers 22, 2577-2637.
  4. Beem, K.M., Richardson, D.C., and Rajagopalan, K.V. (1977). Metal sites of copper-zinc superoxide dismutase. Biochemistry 16, 1930-1936.
  5. Humphrey, W., Dalke, A., and Schulten, K. (1996). VMDvisual molecular dynamics. J. Mol. Graphics 14, 33-38.
  6. Sayle, R.A., and Milner-White, E.J. (1995). RASMOL: biomolecular graphics for all. Trends Biochem. Sci. 20, 374-376.
  7. Herra'ez, A. (2006). Biomolecules in the computer: jmol to the rescue. Biochem. Educ. 34, 255-261.
  8. Bernstein, H.J. (2000). Recent changes to RasMol, recombining the variants. Trends Biochem. Sci. 25, 453-455.
  9. Henrick, K. et al. (2008). Remediation of the protein data bank archive. Nar. 36, D426-433.
  10. O'Donoghue, S.I., Meyer, J.E., Schafferhans, A., and Fries, K. (2004). The SRS 3D module: integrating structures, sequences, and features. Bioinformatics 20, 2476-2478.
  11. Westbrook, J., Feng, Z., Chen, L., Yang, H., and Berman, H.M. (2003). The protein data bank and structural genomics. Nar. 31, 489-491.