| METHOD about: | ../../doc/explain_methods.html#PX_about_scratch |
| METHOD url: | SCRATCH (SSpro3) |
| METHOD quote: | G Pollastri, D Przybylski, B Rost, P Baldi:: Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins, 47, 228-335, 2002 |
| TYPE : | sec |
| NPROT : | 168 |
| NWEEKS : | 42 |
| AVE_Q3 : | 75.6 |
| AVE_SOV: | 72.1 |
| NOTE 1 : | here ALL results obtained for scratch are given, i.e. NOT those for a common subset! |
| NOTE 2 : | all proteins evaluated had no SIGNIFICANT sequence identity to any protein of previously known structure! |
| type | date | sots | id | Q3 | Q3H%o | Q3H%p | Q3E%o | Q3E%p | Q3L%o | Q3L%p | sov | sovH | sovE | sovL | BAD | info | infoO | infoP | corrH | corrE | corrL | class | contDH | contDE |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| sec | 2004_04_28 | dssp | psum | 75.5 | 81 | 82 | 65 | 72 | 78 | 73 | 72.0 | 77.9 | 73.8 | 67.9 | 3.3 | 0.36 | 0.36 | 0.35 | 0.70 | 0.61 | 0.58 | 8273.8 | 7.7 | 6.3 |
| sec | 2004_04_28 | dssp | sig | 11.3 | 35 | 34 | 41 | 46 | 15 | 15 | 16.2 | 26.3 | 27.7 | 17.3 | 6.5 | 0.16 | 0.17 | 0.16 | 0.26 | 0.30 | 0.20 | 8215.6 | 8.5 | 7.9 |
| sec | 2004_04_28 | dssp | errsig | 0.87 | 2 | 2 | 3 | 3 | 1 | 1 | 1.2 | 2.0 | 2.1 | 1.3 | 0.50 | 0.01 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 633.8 | 0.66 | 0.61 |
| Type | Method | Month | Nprot | Average Q3 for month | File with details for month |
|---|---|---|---|---|---|
| sec | scratch | ALL | 168 | 75.6 | |
| sec | scratch | 2003_07 | 5 | 82.9 | old/2003_07_scratch.html |
| sec | scratch | 2003_08 | 5 | 77.0 | old/2003_08_scratch.html |
| sec | scratch | 2003_11 | 22 | 76.8 | old/2003_11_scratch.html |
| sec | scratch | 2003_12 | 13 | 75.7 | old/2003_12_scratch.html |
| sec | scratch | 2004_01 | 11 | 70.0 | old/2004_01_scratch.html |
| sec | scratch | 2004_02 | 19 | 77.4 | old/2004_02_scratch.html |
| sec | scratch | 2004_03 | 13 | 75.5 | old/2004_03_scratch.html |
| sec | scratch | 2004_04 | 4 | 80.2 | old/2004_04_scratch.html |
| sec | scratch | ALL | 168 | 75.6 |
| psum | percentage over all proteins |
| sig | standard deviation |
| errsig | significant difference (to distinguish between two methods) |
| type | prediction type |
| date | date when added [yyyy_mm_dd] |
| sots | standard of truth |
| id | identifier of protein |
| Q3 | three-state per-residue accuracy (percentage of correctly predicted residues) |
| Q3H%o | correctly predicted helix residues (percentage of helix observed) |
| Q3H%p | correctly predicted helix residues (percentage of helix predicted) |
| Q3E%o | correctly predicted strand residues (percentage of helix observed) |
| Q3E%p | correctly predicted strand residues (percentage of helix predicted) |
| Q3L%o | correctly predicted loop residues (percentage of helix observed) |
| Q3L%p | correctly predicted loop residues (percentage of helix predicted) |
| sov | per segment accuracy (three states) |
| sovH | per segment accuracy for helix residues |
| sovE | per segment accuracy for strand residues |
| sovL | per segment accuracy for non-regular residues |
| BAD | percentage of confused HELIX/STRAND residues (helix predicted as strand, strand predicted as helix) |
| infoO | information index accuracy (percentage of observed) |
| infoP | information index accuracy (percentage of predicted) |
| corrH | Matthews correlation index for helix |
| corrE | Matthews correlation index for strand |
| corrL | Matthews correlation index for loop |
| var | variance over all proteins (1/N-1)*( score(i) - |
| sig | sigma (standard deviation) over all proteins (sqrt[var]) |
| errsig | significant differences ( standard dev / sqrt(Nprot) ) |