Searching protein structure databases has come of age

The number of protein structures known in atomic detail has increased from one in 1960 (Kendrew, J.C., Strandberg, B.E., Hart, R.G., Davies, D.R., Phillips, D.C., Shore, V.C. Nature (London) 185:422-427, 1960) to more than 1000 in 1994. The rate at which new structures are being published exceeds one a day as a result of recent advances in protein engineering, crystallography, and spectroscopy. More and more frequently, a newly determined structure is similar in fold to a known one, even when no sequence similarity is detectable. A new generation of computer algorithms has now been developed that allows routine comparison of a protein structure with the database of all known structures. Such structure database searches are already used daily and they are beginning to rival sequence database searches as a tool for discovering biologically interesting relationships.