| 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 : | 207 |
| NWEEKS : | 64 |
| AVE_Q3 : | 76.2 |
| AVE_SOV: | 71.6 |
| 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 | 2008_04_09 | dssp | psum | 76.1 | 82 | 81 | 60 | 70 | 75 | 72 | 71.6 | 78.9 | 73.3 | 69.0 | 3.6 | 0.35 | 0.35 | 0.35 | 0.68 | 0.58 | 0.57 | 8164.2 | 7.9 | 6.8 |
| sec | 2008_04_09 | dssp | sig | 11.2 | 33 | 32 | 41 | 47 | 15 | 16 | 15.8 | 22.9 | 29.2 | 17.4 | 6.5 | 0.16 | 0.17 | 0.17 | 0.23 | 0.32 | 0.20 | 8102.2 | 8.5 | 9.0 |
| sec | 2008_04_09 | dssp | errsig | 0.78 | 2 | 2 | 2 | 3 | 1 | 1 | 1.1 | 1.5 | 2.0 | 1.2 | 0.45 | 0.01 | 0.01 | 0.01 | 0.01 | 0.02 | 0.01 | 563.1 | 0.59 | 0.62 |
| Type | Method | Month | Nprot | Average Q3 for month | File with details for month |
|---|---|---|---|---|---|
| sec | scratch | ALL | 207 | 76.2 | |
| 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 | 11 | 78.5 | old/2004_04_scratch.html |
| sec | scratch | 2004_05 | 6 | 74.4 | old/2004_05_scratch.html |
| sec | scratch | 2004_06 | 7 | 75.0 | old/2004_06_scratch.html |
| sec | scratch | 2004_07 | 10 | 78.1 | old/2004_07_scratch.html |
| sec | scratch | 2004_08 | 17 | 77.6 | old/2004_08_scratch.html |
| sec | scratch | 2004_09 | 4 | 68.6 | old/2004_09_scratch.html |
| sec | scratch | 2004_10 | 1 | 71.4 | old/2004_10_scratch.html |
| sec | scratch | 2004_11 | 4 | 71.8 | old/2004_11_scratch.html |
| sec | scratch | 2004_12 | 1 | 86.5 | old/2004_12_scratch.html |
| sec | scratch | 2005_02 | 1 | 43.5 | old/2005_02_scratch.html |
| sec | scratch | 2005_03 | 18 | 78.2 | old/2005_03_scratch.html |
| sec | scratch | 2005_04 | 12 | 77.3 | old/2005_04_scratch.html |
| sec | scratch | 2005_05 | 12 | 74.8 | old/2005_05_scratch.html |
| sec | scratch | 2005_06 | 4 | 76.5 | old/2005_06_scratch.html |
| sec | scratch | 2005_07 | 15 | 75.5 | old/2005_07_scratch.html |
| sec | scratch | 2005_08 | 15 | 76.1 | old/2005_08_scratch.html |
| sec | scratch | ALL | 207 | 76.2 |
| 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) ) |