| METHOD about: | ../../doc/explain_methods.html#PX_about_samt99_sec |
| METHOD url: | SAM-T99sec |
| METHOD quote: | K Karplus, C Barrett, and R Hughey:: Hidden Markov Models for Detecting Remote Protein Homologies, Bioinformatics, 14, 846-856, 1998 |
| TYPE : | sec |
| NPROT : | 543 |
| NWEEKS : | 100 |
| AVE_Q3 : | 75.6 |
| AVE_SOV: | 70.8 |
| NOTE 1 : | here ALL results obtained for samt99_sec 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 | 2002_10_07 | dssp | psum | 75.5 | 84 | 77 | 63 | 77 | 74 | 72 | 70.8 | 74.4 | 70.9 | 65.2 | 2.2 | 0.36 | 0.35 | 0.37 | 0.69 | 0.63 | 0.54 | 8379.3 | 6.7 | 5.5 |
| sec | 2002_10_07 | dssp | sig | 10.0 | 32 | 30 | 34 | 40 | 17 | 15 | 14.6 | 25.7 | 26.7 | 17.6 | 3.8 | 0.25 | 0.16 | 0.44 | 0.26 | 0.25 | 0.18 | 8303.3 | 8.0 | 6.4 |
| sec | 2002_10_07 | dssp | errsig | 0.43 | 1 | 1 | 1 | 1 | 0.75 | 0.67 | 0.62 | 1.1 | 1.1 | 0.75 | 0.16 | 0.01 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 356.3 | 0.34 | 0.27 |
| Type | Method | Month | Nprot | Average Q3 for month | File with details for month |
|---|---|---|---|---|---|
| sec | samt99_sec | ALL | 543 | 75.6 | |
| sec | samt99_sec | 2000_06 | 4 | 83.8 | old/2000_06_samt99_sec.html |
| sec | samt99_sec | 2000_07 | 20 | 77.9 | old/2000_07_samt99_sec.html |
| sec | samt99_sec | 2000_08 | 17 | 76.8 | old/2000_08_samt99_sec.html |
| sec | samt99_sec | 2000_09 | 4 | 68.2 | old/2000_09_samt99_sec.html |
| sec | samt99_sec | 2000_10 | 18 | 75.8 | old/2000_10_samt99_sec.html |
| sec | samt99_sec | 2000_11 | 23 | 76.1 | old/2000_11_samt99_sec.html |
| sec | samt99_sec | 2000_12 | 27 | 79.2 | old/2000_12_samt99_sec.html |
| sec | samt99_sec | 2001_01 | 15 | 77.2 | old/2001_01_samt99_sec.html |
| sec | samt99_sec | 2001_02 | 13 | 70.7 | old/2001_02_samt99_sec.html |
| sec | samt99_sec | 2001_03 | 26 | 73.3 | old/2001_03_samt99_sec.html |
| sec | samt99_sec | 2001_04 | 8 | 76.2 | old/2001_04_samt99_sec.html |
| sec | samt99_sec | 2001_05 | 9 | 75.2 | old/2001_05_samt99_sec.html |
| sec | samt99_sec | 2001_06 | 13 | 71.7 | old/2001_06_samt99_sec.html |
| sec | samt99_sec | 2001_07 | 14 | 77.3 | old/2001_07_samt99_sec.html |
| sec | samt99_sec | 2001_08 | 35 | 75.0 | old/2001_08_samt99_sec.html |
| sec | samt99_sec | 2001_09 | 27 | 76.9 | old/2001_09_samt99_sec.html |
| sec | samt99_sec | 2001_10 | 6 | 63.5 | old/2001_10_samt99_sec.html |
| sec | samt99_sec | 2001_11 | 11 | 72.9 | old/2001_11_samt99_sec.html |
| sec | samt99_sec | 2001_12 | 60 | 78.2 | old/2001_12_samt99_sec.html |
| sec | samt99_sec | 2002_01 | 13 | 79.9 | old/2002_01_samt99_sec.html |
| sec | samt99_sec | 2002_02 | 22 | 72.0 | old/2002_02_samt99_sec.html |
| sec | samt99_sec | 2002_03 | 19 | 76.1 | old/2002_03_samt99_sec.html |
| sec | samt99_sec | 2002_04 | 18 | 71.4 | old/2002_04_samt99_sec.html |
| sec | samt99_sec | 2002_05 | 24 | 71.2 | old/2002_05_samt99_sec.html |
| sec | samt99_sec | 2002_06 | 15 | 78.4 | old/2002_06_samt99_sec.html |
| sec | samt99_sec | 2002_07 | 18 | 78.4 | old/2002_07_samt99_sec.html |
| sec | samt99_sec | 2002_08 | 16 | 77.0 | old/2002_08_samt99_sec.html |
| sec | samt99_sec | 2002_09 | 12 | 74.9 | old/2002_09_samt99_sec.html |
| sec | samt99_sec | ALL | 543 | 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) ) |