title: Further evidence for the likely completeness of the library of solved single domain protein structures.
abstract: Recent studies questioned whether the Protein Data Bank (PDB) contains all compact, single domain protein structures. Here, we show that all quasi-spherical, QS, random protein structures devoid of secondary structure are in the PDB and are excellent templates for all native PDB proteins up to 250 residues. Because QS templates have a similar global contour as native, TASSER can refine 98% (90%) of those whose TM-score is 0.4 (0.35) to structures greater than or equal to the 0.5 TM-score threshold (0.74 (0.64) mean TM-score) for CATH/SCOP assignment. On the basis of this and the fact that, at a TM-score of 0.4, 83% (90%) of all (internal) core secondary structure elements are recovered, a 0.40 TM-score is an appropriate fold similarity assignment threshold. Despite the claims of Taylor, Trovato, and Zhou that many of their structures lack a PDB counterpart, using fr-TM-align, at a 0.45 (0.5) TM-score threshold, essentially all (most) are found in the PDB. Thus, the conclusion that the PDB is likely complete is further supported.
authors.affiliation: Center for the Study of Systems Biology, Georgia Institute of Technology, 250 14th Street NW, Atlanta, Georgia 30318, USA. skolnick@gatech.edu
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Skolnick
authors.forename: Hongyi
authors.initials: H
authors.lastname: Zhou
authors.forename: Michal
authors.initials: M
authors.lastname: Brylinski
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D008958:Models, Molecular; D019151:Peptide Library; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
chemical_list: D019151:Peptide Library; D011506:Proteins