Knowledge-based prediction of protein structures

We propose a knowledge-based approach to the prediction of protein structures in cases where there is no sequence-homology to proteins with known spatial structure. Using methods from Artificial Intelligence we attempt to take into account long-range interactions within the prediction process. This allows not only the assignment of secondary but also of supersecondary structure elements. In particular, the patterns used as conditions of prediction rules are generated by learning methods from information contained in the Protein Data Base. Patterns on higher levels of the protein structure hierarchy are used as constraints to reduce the combinatorial search space. These patterns may also be used to search for specified structure motifs by interactive retrieval.