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Further Evidence for the Likely Completeness of the Library of Solved Single Domain Protein Structures
| Content Provider | PubMed Central |
|---|---|
| Author | Skolnick, Jeffrey Zhou, Hongyi Brylinski, Michal |
| Abstract | Recent studies questioned whether the 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 similar global contour as native, TASSER can refine 98% (90%) of those whose TM-score is 0.4 (0.35) to structures ≥ the 0.5 TM-score threshold (0.74 (0.64) mean TM-score) for CATH/SCOP assignment. Based on 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 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. |
| Related Links | http://dx.doi.org/10.1039/c1cp21140d |
| Starting Page | 17044 |
| File Format | |
| ISSN | 14639076 |
| e-ISSN | 14639084 |
| Journal | Physical Chemistry Chemical Physics |
| Issue Number | 38 |
| Volume Number | 13 |
| Language | English |
| Publisher Date | 2011-01-01 |
| Access Restriction | Open |
| Subject Keyword | Physical and Theoretical Chemistry Physics and Astronomy(all) Research in Higher Education |
| Content Type | Text |
| Resource Type | Article |
| Subject | Physics and Astronomy Physical and Theoretical Chemistry |
