Fold predictions for bacterial genomes

Fold assignments for newly sequenced genomes belong to the most important a nd interesting applications of the booming field of protein structure predi ction. We present a brief survey and a discussion of such assignments compl eted to date, using as an example several fold assignment projects for prot eins from the Escherichia coli genome. This review focuses on steps that ar e necessary to go beyond the simple assignment projects and into the develo pment of tools extending our understanding of functions of proteins in newl y sequenced genomes. This paper also discusses several problems seldom addr essed in the literature, such as the problem of domain prediction and compl ementary predictions (e.g., transmembrane regions and flexible regions) and cross-correlation of predictions from different servers. The influence of sequence and structure database growth on prediction success is also addres sed. Finally, we discuss the perspectives of the field in the context of ma ssive sequence and structure determination projects, as well as the develop ment of novel prediction methods. (C) 2001 Academic Press.