The ups and downs of protein topology; rapid comparison of protein structure

Protein topology can be described at different levels. At themost fundamental level, it is a sequence of secondary structureelements (a `primary topology string'). Searching predictedprimary topology strings against a library of strings from knownprotein structures is the basis of some protein fold recognitionmethods. Here a method known as TOPSCAN is presented for rapidcomparison of protein structures. Rather than a simple two-letteralphabet (encoding strand and helix), more complex alphabetsare used encoding direction, proximity, accessibility and lengthof secondary elements and loops in addition to secondary structure.Comparisons are made between the structural information contentof primary topology strings and encodings which contain additionalinformation (`secondary topology strings'). The algorithm isextremely fast, with a scan of a large domain against a libraryof more than 2000 secondary structure strings completing in