An augmented ribbon model of protein structure

Abstract

In this paper, work on a new model,an augmented ribbon model, for describing a number of features of primary, secondary, and super-secondary protein structure in a qualitative but mathematically rigorous way is discussed. The structural features that can be treated by the model include connectivity, directionality, chirality, orientation, and proximity which, in many cases, are difficult to deal with using more traditional structural representations (e.g. “wireframe”, “ball-and-stick”, or “space-filling CPK”). In practice, the information encoded in the augmented ribbon model is represented by a labelled, directed graph (digraph) which provides an efficient means for storing and analyzing the information on computers. This opens the way to computer-based analyses of proteins and for the application of similarity methods that have been shown to be quite useful in treating small molecules.