Representing protein and peptide structures with parallel-coordinates

✍ Scribed by Becker, Oren M.

• Book ID: 101220680
• Publisher: John Wiley and Sons
• Year: 1997
• Tongue: English
• Weight: 280 KB
• Volume: 18
• Category: Article
• ISSN: 0192-8651
• DOI: 10.1002/(sici)1096-987x(19971130)18:15<1893::aid-jcc5>3.0.co;2-j

✦ Synopsis

Graphical representation of molecular conformations is an important tool used by chemists to gain molecular insight. In spite of today's enhanced computer graphics there are still situations, such as in multiple conformation displays, in which standard visualization techniques are limited.

Ž5 . Parallel-coordinate -coords representation, which 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 axes are drawn parallel rather than perpendicular to each other, allowing many axes to be placed and seen. This mapping procedure has unique geometric properties and useful relationships to the original space. In this article, we apply the parallel-coordinate representation for presenting peptide and protein structural conformations. In particular, we demonstrate the usefulness of parallel-coordinates in the context of conformational analysis where this representation, combined with multiple filters, allows nontrivial 5 clustering of data points, leading to new observations. The -coords Ž . representation is also demonstrated as a tool for two-dimensional 2D representation of protein secondary structure and for identification of disulfidebonded pairs in protein structures. Regardless of the application, an advantage 5 of the -coords approach is that it retains its inherent simplicity and ease of use, and requires little or no software development.