A visualization ToolKit based application for representing macromolecular surfaces

Abstract

Macromolecular structural analysis has been used for a long time, in particular for proteins, with the aim of correlating three dimensional structures with possible functions and interactions. An innovative approach is to tackle these aspects by working on macromolecular surfaces instead of using amino acid or atomic configurations directly, because protein interaction is mainly driven by the macromolecular external characteristics. However, it is difficult to work with surfaces because applications for molecular visualization lack appropriate functions to manipulate these data structures properly. In this paper we describe a visualization pipeline to represent molecular surfaces in three-dimensional space. The pipeline relies on the Visualization Toolkit libraries, and provides a high level functions and easy user interface. This software has been developed in the context of a surface analysis project, but its classes and methods can be used and integrated in a wide range of applications. © 2009 Springer Berlin Heidelberg.