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J Phys Chem B. 2012 Jun 14;116(23):6654-64. doi: 10.1021/jp211052j. Epub 2012 Feb 13.

Further evidence for the likely completeness of the library of solved single domain protein structures.

Author information

1
Center for the Study of Systems Biology, Georgia Institute of Technology, 250 14th Street NW, Atlanta, Georgia 30318, USA. skolnick@gatech.edu

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.

PMID:
22272723
PMCID:
PMC3351587
DOI:
10.1021/jp211052j
[Indexed for MEDLINE]
Free PMC Article

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