A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains labor intensive and relies on an expert's ability to derive and evaluate a protein scene model. In this paper, the problem of protein structure determination is formulated as an exercise in scene analysis. A computational methodology is presented in which a 3D image of a protein is segmented into a graph of critical points. Bayesian and certainty factor approaches are described and used to analyze critical point graphs and identify meaningful substructures, such as alpha-helices and beta-sheets. Results of applying the methodologies to protein images at low and medium resolution are reported. The research is related to approaches to representation, segmentation and classification in vision, as well as to top-down approaches to protein structure prediction.

An approach to knowledge discovery in complex molecular databases is described. The machine learning paradigm used is structured concept formation, in which object's described in terms of components and their interrelationships are clustered and organized in a knowledge base. Symbolic images are used to represent classes of structured objects. A discovered molecular knowledge base is successfully used in the interpretation of a high resolution electron density map.>