The study of the structure and function of proteins serves up many problems that offer challenges and opportunities for computational and statistical research. I will overview my experiences in several such problem domains, ranging from domains where off-the-shelf ideas can be fruitfully applied to domains that require new thinking. These are:

1. the identification of active sites in enzymes;
2. the modeling of protein backbone configurations;
3. the prediction of molecular function based on phylogeny;
4. alignment and phylogenetic inference.