Surveys of Known Protein Structures

A common approach in the study of secondary structure or small pieces of structure is to survey known protein structures for all instances of such structures and then to analyze those found. Such an approach has been taken for PPII helices (Adzhubei and Sternberg, 1993 Stapley and Creamer, 1999) and for residues that adopt the PPII conformation but are not necessarily part of PPII helices (Sreerama and Woody,... 

A survey of known three-dimensional structure of proteins shows that a sizeable portion of them contain several apparently independent folding units, usually referred to as domains . 

The 16 possible motifs shown in Figure 2.21b never occur. Even if this database is limited compared with the universe of existing proteins, the survey clearly demonstrates that a few topological arrangements occur much more frequently than others, and that most possible complex motifs never occur or occur only in a few cases. In 1995 a preliminary survey of a much larger database of known structures yielded the same basic conclusions. 

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