In this lecture, I discuss the challenges of designing new proteins that fold into a particular structure or perform a particular function. One method is to computationally design a protein based solely upon our knowledge of amino acids and protein folding, a hard task but one which has had recent successes. Another approach is to screen combinatorial libraries of proteins for a desired function. In particular, I will discuss how structure-based computational methods can allow for high...

This video was produced by GILDA and INFN to show the use of Rosetta protein-folding software on the EUChinaGRID cyberinfrastructure via the GENIUS grid portal.

A simple classification scheme that uses only the presence or absence of a protein domain architecture has been used to determine the phylogeny of 174 complete genomes. The method correctly divides the 174 taxa into Archaea, Bacteria, and Eukarya and satisfactorily sorts most of the major groups within these superkingdoms. The most challenging problem involved 119 Bacteria, many of which have reduced genomes. When a weighting factor was used that takes account of difference in genome size...