| 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 : | 329 |
| NWEEKS : | 86 |
| AVE_Q3 : | 75.5 |
| AVE_SOV: | 71.5 |
| 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 | 2004_04_28 | dssp | psum | 75.4 | 84 | 78 | 63 | 74 | 74 | 73 | 71.4 | 76.7 | 73.0 | 66.6 | 2.7 | 0.35 | 0.36 | 0.35 | 0.69 | 0.61 | 0.54 | 8632.2 | 7.3 | 6.4 |
| sec | 2004_04_28 | dssp | sig | 10.7 | 34 | 32 | 38 | 44 | 17 | 15 | 15.5 | 26.1 | 27.4 | 18.7 | 4.8 | 0.17 | 0.17 | 0.17 | 0.25 | 0.28 | 0.19 | 8558.9 | 7.7 | 7.1 |
| sec | 2004_04_28 | dssp | errsig | 0.59 | 1 | 1 | 2 | 2 | 0.97 | 0.84 | 0.85 | 1.4 | 1.5 | 1.0 | 0.26 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 471.8 | 0.42 | 0.39 |
| Type | Method | Month | Nprot | Average Q3 for month | File with details for month |
|---|---|---|---|---|---|
| sec | samt99_sec | ALL | 329 | 75.5 | |
| sec | samt99_sec | 2001_04 | 1 | 78.2 | old/2001_04_samt99_sec.html |
| sec | samt99_sec | 2003_07 | 5 | 81.8 | old/2003_07_samt99_sec.html |
| sec | samt99_sec | 2003_08 | 5 | 78.0 | old/2003_08_samt99_sec.html |
| sec | samt99_sec | 2003_11 | 22 | 76.1 | old/2003_11_samt99_sec.html |
| sec | samt99_sec | 2003_12 | 18 | 79.8 | old/2003_12_samt99_sec.html |
| sec | samt99_sec | 2004_01 | 12 | 74.7 | old/2004_01_samt99_sec.html |
| sec | samt99_sec | 2004_02 | 19 | 76.1 | old/2004_02_samt99_sec.html |
| sec | samt99_sec | 2004_03 | 13 | 77.7 | old/2004_03_samt99_sec.html |
| sec | samt99_sec | 2004_04 | 4 | 83.5 | old/2004_04_samt99_sec.html |
| sec | samt99_sec | ALL | 329 | 75.5 |
| 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) ) |