EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, U.K.
The comparison of the 3D structures of protein molecules poses a complex algorithmic problem. Its solution provides biologists with computational tools to organize the rapidly growing set of thousands of known protein structures, to identify new types of protein architecture, and to discover unexpected evolutionary relationships between protein molecules reaching back billions of years. Protein structure comparison also improves tools for identifying gene functions in genome databases by defining the essential sequence-structure features of a protein family. An exhaustive all-on-all structure comparison using the Dali algorithms provides a map of physical attractor regions in the abstract shape space of proteins, with implications for the processes of protein folding and evolution. Based on a paper co-authored with Liisa Holm, Science 273 (1996) 595-602. See also http://www.sciencemag.org/science/scripts/display/full/273/5275/595.html and http://www.embl-heidelberg.de/dali.