REPRESENTING PROTEIN AND PEPTIDE STRUCTURES WITH PARALLEL-COORDINATES

Graphical representation of molecular conformations is an important to ol used by chemists to gain molecular insight. In spite of today's enh anced computer graphics there are still situations, such as in multipl e conformation displays, in which standard visualization techniques ar e Limited. Parallel-coordinate (parallel to-coords) representation, wh ich was originally developed for visualizing multivariant datasets in fields other than chemistry, offers an alternative basis for graphical representation of molecular structures. In parallel-coordinates the a xes are drawn parallel rather than perpendicular to each other, allowi ng many axes to be placed and seen. This mapping procedure has unique geometric properties and useful relationships to the original space. I n this article, we apply the parallel-coordinate representation for pr esenting peptide and protein structural conformations. In particular, we demonstrate the usefulness of parallel-coordinates in the context o f conformational analysis where this representation, combined with mul tiple filters, allows nontrivial clustering of data points, leading to new observations. The parallel to-coords representation is also demon strated as a tool for two-dimensional (2D) representation of protein s econdary structure and for identification of disulfide-bonded pairs in protein structures. Regardless of the application, an advantage of th e parallel to-coords approach is that it retains its inherent simplici ty and ease of use, and requires little or no software development. (C ) 1997 John Wiley & Sons, Inc.