How representative are the known structures of the proteins in a complete genome?
Gerstein M Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA. Mark.Gerstein@yale.edu BACKGROUND: Determining how representative the known structures are of the proteins encoded by a complete genome is important for assessing to what extent our current picture of protein stability and folding is overly influenced by biases in the structure databank (PDB). It is also important for improving database-based methods of structure prediction and genome annotation. RESULTS: The known structures are compared to the proteins encoded by eight complete microbial genomes in terms of simple statistics such as sequence length, composition and secondary structure. The known structures are represented by a collection of nonhomologous domains from the PDB and a smaller list of ‘biophysical proteins’ on which folding experiments have concentrated. The proteins encoded by the genomes are considered as a whole and divided into various regions, such as known-struct
