Table 1.
Summary of the content and description of different PPT-DB databases
| Database | Description | Database | Description |
|---|---|---|---|
| 2° Structure (cytoplasmic) 15 002 sequences | 3-state 2° structure assignments obtained by VADAR (25) for non-membrane proteins | Signal Peptide (Eukaryotic, Gram+, Gram−) 23 067 sequences | 2-state signal peptide assignments obtained from SwissProt comment fields — grouped via organism type |
| EVA 2° Structure Test Set 7117 sequences | 3-state 2° structure assignments via VADAR (25) for EVA's sequence-unique proteins (19) | Accessible Surface Area (integerized) 14 871 sequences | Residue-specific accessible surface area obtained via VADAR (25) and scaled to values between 0 and 9 |
| 2° Structure (membrane helix) 254 sequences | 2-state 2° structure assignments obtained via VADAR (25) for helical membrane proteins | Accessible Surface Area (%) 14871 sequences | Residue-specific accessible surface area obtained via VADAR (25) and converted to percentage values |
| TMH Benchmark Test Set 2247 sequences | 2-state 2° structure assignments for transmembrane helices from TMH Benchmark (20) | B-factor (integerized) 10 332 sequences | Residue-specific B-factors obtained directly from PDB files of X-ray structures and scaled to values from 0 to 9 |
| 2° Structure (membrane barrel) 41 sequences | 2-state 2° structure assignments obtained by VADAR (25) for trans-membrane barrel proteins | B-factor 10 332 sequences | Residue-specific B-factors obtained directly from PDB (26) files of non-membrane X-ray structures |
| % 2° Structure (cytoplasmic) 15 002 sequences | 3-state 2° structure content obtained by VADAR (25) for non-membrane proteins | RMSF (integerized) 2134 sequences | Scaled (0–9) residue-specific RMSF values determined from NMR structures via SuperPose (29) |
| Beta Turns 14 571 sequences | 5-state beta-turn assignments obtained via VADAR (25) for non-membrane proteins | RMSF 2134 sequences | Residue-specific root mean square fluctuation (RMSF) determined from NMR structures via SuperPose (29) |
| Coiled-coil 824 sequences | 2-state, positional assignments for coiled coil regions from the Paircoil2 training set (15) | Order Parameter (integerized) 9800 sequences | Scaled (0–9) residue-specific order parameter (model free) determined using Contact Model method (2) |
| Edge/Central Beta Strands 13 255 sequences | 2-state beta strand type assignments obtained by VADAR (25) and pattern recognition programs | Order Parameter 9800 sequences | Residue-specific order parameter (model free) determined using Contact Model method (2) |
| Beta Hairpins 8600 sequences | 2-state beta hairpin assignments obtained by VADAR (25) and pattern recognition programs | Contact Order 14 769 sequences | Contact order calculated using method of Plaxco et al. (1) directly from PDB coordinates |
| Disulfide Bonds 2785 sequences | Disulfide bond pairings obtained by VADAR (25) and PDB comment fields | Folding Rate 83 sequences | Experimentally measured folding rates (ln[kf]) obtained from multiple sources (1,3) |
| SPdb (Eukaryotic, Gram+, Gram−) 2590 sequences | Experimentally verified 2-state signal peptide assignments obtained from the SPdb (21) grouped via organism type | 3D Folding Decoys 52 sequences | PDB coordinates for misfolded or improperly folded proteins generated via different 3D prediction tools |