KING (Kinemage, Next Generation): a versatile interactive molecular and scientific visualization program

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.

Figure 1

KiNG graphical user interface. An image of the KiNG graphical user interface, showing the Backrub tool being used to reconstruct an alternate conformation of a lysine residue in a protein structure (PDB: 1US0). Contact dots from Probe are shown (as dots and small spikes). The electron density is shown in gray wire-mesh, the original model in white and cyan, and the active model in orange. Pop-up windows for controlling aspects of the backrub motion, the electron density, and the contact dots are also visible.

Figure 2

Information visualization capabilities of KiNG. Figures illustrating different types of representations in KiNG of the same data: all 21 rotamers of Arg with chi1 trans, from an updated version (unpublished) of our protein sidechain rotamer library. Two custom green colors were defined for this figure (see “Materials and Methods”). This figure is also available in interactive kinemage format, in Supporting Information. Panel A shows stick representations of different arginine rotamers with their backbone atoms superimposed. Backbone is colored in white, with the different sidechain rotamers in different colors. Balls are used to indicate nitrogen and oxygen backbone atoms. Text labels were added using Adobe Photoshop. Panel B shows a 3D plot of the chi2 through chi4 dihedral angles of the arginine rotamers shown in A, with identical coloring. The data points are represented by balls. Contours were drawn using kin3Dcont. Axis text labels were added using Adobe Photoshop. Panels C and D show the parallel coordinate representation of chi1 through chi4 of the arginine rotamers, where each polyline spanning the four axes represents one data point. Panel D shows the same data as Panel C, but with transparency increased. The tick marks and degree indicators were added using Adobe Photoshop.

Figure 3

An example of ribbon graphics in KiNG. Screen-captured 2D image of a ribbon diagram of staphylococcal alpha-hemolysin, a heptameric transmembrane pore (PDB: 7AHL), viewed down the pore. This figure is also available in interactive kinemage format, in Supporting Information.