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Keywords:

  • interactive molecular graphics;
  • kinemage graphics;
  • backrub motion;
  • all-atom contact dots;
  • Molikin;
  • Mage;
  • Java

Abstract

Proper visualization of scientific data is important for understanding spatial relationships. Particularly in the field of structural biology, where researchers seek to gain an understanding of the structure and function of biological macromolecules, it is important to have access to visualization programs which are fast, flexible, and customizable. We present KiNG, a Java program for visualizing scientific data, with a focus on macromolecular visualization. KiNG uses the kinemage graphics format, which is tuned for macromolecular structures, but is also ideal for many other kinds of spatially embedded information. KiNG is written in cross-platform, open-source Java code, and can be extended by end users through simple or elaborate “plug-in” modules. Here, we present three such applications of KiNG to problems in structural biology (protein backbone rebuilding), bioinformatics of high-dimensional data (e.g., protein sidechain chi angles), and classroom education (molecular illustration). KiNG is a mature platform for rapidly creating and capitalizing on scientific visualizations. As a research tool, it is invaluable as a test bed for new methods of visualizing scientific data and information. It is also a powerful presentation tool, whether for structure browsing, teaching, direct 3D display on the web, or as a method for creating pictures and videos for publications. KiNG is freely available for download at http://kinemage.biochem.duke.edu.