A knowledge-based architecture for protein sequence analysis and structure prediction

Methods for analyzing the amino-acid sequence of a protein for the purposes of predicting its three-dimensional structure were systematically analyzed using knowledge engineering techniques. The resulting entities (data) and relations (processing methods and constraints) have been represented within a generalized dependency network consisting of 29 nodes and over 100 links. It is argued that such a representation meets the requirements of knowledge-based systems in molecular biology. This network is used as the architecture for a prototype knowledge-based system that simulates logically the processes used in protein structure prediction. Although developed specifically for applications in protein structure prediction, the network architecture provides a strategy for tackling the general problem of orchestrating and integrating the diverse sources of knowledge that are characteristic of many areas of science.