Searching for the ideal forms of proteins

A modification of the Structure Alignment Program (SAP), combined with a no vel automatic method for the definition of structural elements, correctly i dentified the core folds of a variety of small beta/alpha proteins when com pared with a series of ideal architectures. This approach opens the possibi lity of not just determining whether one structure is like another, but giv en a range of ideal forms, determining what the protein is. Preliminary stu dies have shown it to work equally well on the all alpha-class and the all- beta class of protein, each of which have corresponding ideal forms. Given the speed of the algorithm, it will be possible to compare all of these aga inst the Protein Structure Database and determine the extent to which the c urrent ideal forms can account for the variety of protein structure. Analys is of the remainder should provide a base for the development of further fo rms.