METHOD about: | ../../../doc/explain_methods.html#PX_about_phd |
METHOD url: | PHD |
TYPE : | sec |
NPROT : | 1599 |
NWEEKS : | 109 |
NOTE 1 : | here ALL results obtained for PHD in month 2001_09 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 | 2001_09 | dssp | ALL_proteins:psum | 70.9 | 74 | 76 | 60 | 63 | 72 | 69 | 66.9 | 66.2 | 65.3 | 63.5 | 4.2 | 0.28 | 0.28 | 0.28 | 0.61 | 0.52 | 0.48 | 7542.2 | 7.8 | 6.1 |
sec | 2001_09 | dssp | ALL_proteins:sig | 10.8 | 31 | 31 | 30 | 32 | 14 | 12 | 14.2 | 27.8 | 26.4 | 14.8 | 5.1 | 0.24 | 0.27 | 0.22 | 0.25 | 0.26 | 0.15 | 7469.2 | 8.9 | 6.8 |
sec | 2001_09 | dssp | ALL_proteins:errsig | 0.27 | 0.79 | 0.79 | 0.76 | 0.82 | 0.35 | 0.31 | 0.35 | 0.69 | 0.66 | 0.37 | 0.13 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 186.7 | 0.22 | 0.17 |
sec | 2001_09 | dssp | THIS_month:psum | 70.7 | 61 | 58 | 55 | 64 | 72 | 66 | 67.9 | 58.7 | 69.5 | 64.6 | 3.6 | 0.29 | 0.28 | 0.29 | 0.56 | 0.57 | 0.47 | 61.7 | 9 | 6.3 |
sec | 2001_09 | dssp | 1e1a:A | 63.5 | 100 | 6 | 51 | 87 | 75 | 65 | 56.9 | 57 | 53 | 61 | 6.4 | 0.16 | 0.19 | 0.14 | 0.23 | 0.47 | 0.40 | 0.0 | 14.0 | 21.0 |
sec | 2001_09 | dssp | 1e8c:A | 80.8 | 89 | 84 | 78 | 79 | 74 | 78 | 81.4 | 92 | 80 | 73 | 0.0 | 0.49 | 0.49 | 0.49 | 0.79 | 0.72 | 0.60 | 100.0 | 2.0 | 0.00 |
sec | 2001_09 | dssp | 1e8p:A | 65.2 | 0 | 0 | 72 | 68 | 80 | 62 | 59.4 | 0 | 92 | 53 | 4.3 | 0.16 | 0.13 | 0.20 | 1.0 | 0.50 | 0.41 | 100.0 | 15.0 | 2.0 |
sec | 2001_09 | dssp | 1e8q:A | 65.2 | 0 | 0 | 72 | 68 | 77 | 62 | 61.3 | 0 | 92 | 54 | 2.1 | 0.16 | 0.13 | 0.19 | 1.0 | 0.50 | 0.36 | 100.0 | 13.0 | 2.0 |
sec | 2001_09 | dssp | 1f45:B | 66.7 | 67 | 100 | 0 | 0 | 69 | 56 | 65.5 | 67 | 0 | 65 | 7.1 | 0.32 | 0.39 | 0.27 | 0.64 | -0.06 | 0.42 | 100.0 | 21.0 | 14.0 |
sec | 2001_09 | dssp | 1fex:A | 62.7 | 64 | 76 | 0 | 0 | 60 | 68 | 73.0 | 74 | 100 | 71 | 5.0 | 0.12 | 0.14 | 0.10 | 0.43 | 1.0 | 0.35 | 100.0 | 8.0 | 13.0 |
sec | 2001_09 | dssp | 1gd5:A | 83.1 | 90 | 73 | 68 | 100 | 83 | 86 | 89.0 | 93 | 80 | 89 | 3.0 | 0.50 | 0.49 | 0.52 | 0.71 | 0.79 | 0.72 | 100.0 | 7.0 | 6.0 |
sec | 2001_09 | dssp | 1gd7:A | 59.6 | 28 | 33 | 67 | 63 | 61 | 62 | 57.7 | 23 | 61 | 64 | 6.4 | 0.14 | 0.14 | 0.14 | 0.21 | 0.38 | 0.31 | 100.0 | 1.0 | 2.0 |
sec | 2001_09 | dssp | 1gd8:A | 78.1 | 95 | 81 | 23 | 100 | 83 | 66 | 79.5 | 93 | 33 | 86 | 8.5 | 0.39 | 0.35 | 0.44 | 0.69 | 0.44 | 0.65 | 0.0 | 9.0 | 15.0 |
sec | 2001_09 | dssp | 1h6k:A | 71.0 | 76 | 80 | 0 | 0 | 62 | 64 | 64.3 | 67 | 0 | 60 | 4.7 | 0.14 | 0.15 | 0.13 | 0.42 | -0.02 | 0.45 | 0.0 | 3.0 | 3.0 |
sec | 2001_09 | dssp | 1h8b:B | 56.5 | 47 | 88 | 0 | 0 | 83 | 35 | 41.7 | 34 | 100 | 85 | 0.0 | 0.06 | 0.07 | 0.06 | 0.27 | 1.0 | 0.27 | 100.0 | 34.0 | 0.00 |
sec | 2001_09 | dssp | 1hfo:A | 68.1 | 61 | 93 | 71 | 73 | 73 | 50 | 65.7 | 72 | 77 | 44 | 1.7 | 0.32 | 0.33 | 0.33 | 0.65 | 0.60 | 0.38 | 0.0 | 13.0 | 0.00 |
sec | 2001_09 | dssp | 1hno:A | 69.9 | 85 | 52 | 80 | 94 | 53 | 77 | 71.0 | 78 | 85 | 57 | 2.7 | 0.38 | 0.38 | 0.39 | 0.49 | 0.82 | 0.44 | 0.0 | 17.0 | 4.0 |
sec | 2001_09 | dssp | 1ho8:A | 64.2 | 93 | 73 | 0 | 0 | 15 | 60 | 29.3 | 40 | 100 | 16 | 0.0 | 0.21 | 0.22 | 0.22 | 0.46 | 1.0 | 0.14 | 100.0 | 16.0 | 11.0 |
sec | 2001_09 | dssp | 1hrk:A | 85.2 | 82 | 93 | 80 | 97 | 90 | 73 | 83.6 | 81 | 92 | 82 | 0.0 | 0.56 | 0.56 | 0.57 | 0.77 | 0.87 | 0.70 | 100.0 | 5.0 | 2.0 |
sec | 2001_09 | dssp | 1hze:A | 76.3 | 0 | 0 | 95 | 76 | 80 | 75 | 79.1 | 0 | 100 | 82 | 4.1 | 0.38 | 0.32 | 0.45 | 1.0 | 0.72 | 0.60 | 0.0 | 13.0 | 10.0 |
sec | 2001_09 | dssp | 1i18:A | 77.3 | 0 | 0 | 90 | 76 | 79 | 77 | 75.9 | 0 | 100 | 69 | 3.0 | 0.33 | 0.28 | 0.38 | 1.0 | 0.68 | 0.60 | 0.0 | 9.0 | 8.0 |
sec | 2001_09 | dssp | 1i8a:A | 70.9 | 21 | 23 | 63 | 84 | 86 | 68 | 67.4 | 25 | 70 | 69 | 4.2 | 0.24 | 0.24 | 0.25 | 0.16 | 0.56 | 0.52 | 100.0 | 0.00 | 11.0 |
sec | 2001_09 | dssp | 1i9g:A | 74.6 | 83 | 69 | 63 | 76 | 76 | 76 | 79.5 | 90 | 73 | 77 | 5.6 | 0.33 | 0.33 | 0.33 | 0.66 | 0.58 | 0.59 | 0.0 | 5.0 | 5.0 |
sec | 2001_09 | dssp | 1iqp:A | 80.1 | 83 | 87 | 65 | 87 | 78 | 65 | 77.9 | 87 | 71 | 61 | 2.4 | 0.36 | 0.36 | 0.37 | 0.62 | 0.73 | 0.59 | 100.0 | 2.0 | 2.0 |
sec | 2001_09 | dssp | 1j75:A | 80.7 | 84 | 100 | 45 | 100 | 100 | 54 | 82.5 | 100 | 54 | 61 | 0.0 | 0.57 | 0.56 | 0.59 | 0.83 | 0.63 | 0.63 | 100.0 | 8.0 | 10.0 |
sec | 2001_09 | dssp | 1j7v:R | 75.6 | 36 | 36 | 77 | 74 | 78 | 80 | 77.2 | 27 | 82 | 77 | 4.3 | 0.25 | 0.26 | 0.26 | 0.32 | 0.55 | 0.60 | 100.0 | 0.00 | 1.0 |
sec | 2001_09 | dssp | 1j8r:A | 61.7 | 100 | 11 | 54 | 85 | 70 | 62 | 69.4 | 100 | 67 | 70 | 9.1 | 0.16 | 0.19 | 0.14 | 0.30 | 0.43 | 0.41 | 0.0 | 16.0 | 20.0 |
sec | 2001_09 | dssp | 1j9y:A | 68.4 | 73 | 76 | 66 | 43 | 65 | 73 | 61.3 | 78 | 62 | 52 | 2.7 | 0.25 | 0.26 | 0.24 | 0.61 | 0.44 | 0.42 | 0.0 | 1.0 | 7.0 |
sec | 2001_09 | dssp | 1jce:A | 62.8 | 72 | 81 | 44 | 62 | 67 | 47 | 62.5 | 75 | 50 | 56 | 4.5 | 0.22 | 0.22 | 0.23 | 0.62 | 0.37 | 0.32 | 0.0 | 4.0 | 8.0 |
sec | 2001_09 | dssp | 1jcg:A | 63.8 | 74 | 79 | 44 | 64 | 68 | 50 | 63.8 | 74 | 50 | 61 | 3.8 | 0.23 | 0.23 | 0.23 | 0.63 | 0.39 | 0.33 | 0.0 | 2.0 | 8.0 |
sec | 2001_09 | dssp | 1jma:A | 61.8 | 26 | 30 | 34 | 60 | 88 | 68 | 46.6 | 29 | 45 | 51 | 10.4 | 0.12 | 0.11 | 0.13 | 0.15 | 0.29 | 0.45 | 100.0 | 2.0 | 13.0 |
sec | 2001_09 | dssp | 1jmt:A | 66.1 | 48 | 100 | 86 | 81 | 83 | 38 | 77.9 | 72 | 100 | 63 | 1.7 | 0.41 | 0.42 | 0.41 | 0.55 | 0.77 | 0.38 | 100.0 | 26.0 | 1.0 |
sec | 2001_09 | dssp | 1jnx:X | 61.8 | 69 | 65 | 70 | 46 | 53 | 69 | 63.6 | 71 | 64 | 57 | 4.8 | 0.17 | 0.18 | 0.17 | 0.49 | 0.45 | 0.33 | 0.0 | 1.0 | 9.0 |
sec | 2001_09 | dssp | 1jr3:A | 80.3 | 90 | 80 | 78 | 64 | 66 | 85 | 78.2 | 77 | 79 | 79 | 3.0 | 0.37 | 0.37 | 0.38 | 0.64 | 0.68 | 0.64 | 100.0 | 6.0 | 1.0 |
sec | 2001_09 | dssp | 1jr3:D | 70.1 | 96 | 67 | 34 | 72 | 40 | 82 | 57.5 | 66 | 39 | 49 | 6.5 | 0.24 | 0.20 | 0.28 | 0.48 | 0.45 | 0.45 | 100.0 | 23.0 | 5.0 |
sec | 2001_09 | dssp | 1jx3:A | 73.2 | 88 | 72 | 68 | 59 | 66 | 80 | 57.8 | 77 | 66 | 49 | 0.0 | 0.36 | 0.37 | 0.35 | 0.70 | 0.55 | 0.47 | 100.0 | 6.0 | 2.0 |
sec | 2001_09 | dssp | 1jx5:A | 76.3 | 0 | 0 | 65 | 64 | 82 | 84 | 72.1 | 0 | 66 | 75 | 1.3 | 0.19 | 0.20 | 0.18 | -0.01 | 0.48 | 0.49 | 100.0 | 1.0 | 0.00 |
sec | 2001_09 | dssp | 1jzt:A | 82.3 | 79 | 87 | 76 | 82 | 86 | 78 | 80.4 | 80 | 80 | 80 | 0.0 | 0.47 | 0.47 | 0.49 | 0.74 | 0.75 | 0.64 | 100.0 | 3.0 | 1.0 |
sec | 2001_09 | dssp | THIS_month:psum | 70.7 | 61 | 58 | 55 | 64 | 72 | 66 | 67.9 | 58.7 | 69.5 | 64.6 | 3.6 | 0.29 | 0.28 | 0.29 | 0.56 | 0.57 | 0.47 | 61.7 | 9 | 6.3 |
sec | 2001_09 | dssp | ALL_proteins:psum | 70.9 | 74 | 76 | 60 | 63 | 72 | 69 | 66.9 | 66.2 | 65.3 | 63.5 | 4.2 | 0.28 | 0.28 | 0.28 | 0.61 | 0.52 | 0.48 | 7542.2 | 7.8 | 6.1 |
sec | 2001_09 | dssp | ALL_proteins:sig | 10.8 | 31 | 31 | 30 | 32 | 14 | 12 | 14.2 | 27.8 | 26.4 | 14.8 | 5.1 | 0.24 | 0.27 | 0.22 | 0.25 | 0.26 | 0.15 | 7469.2 | 8.9 | 6.8 |
sec | 2001_09 | dssp | ALL_proteins:errsig | 0.27 | 0.79 | 0.79 | 0.76 | 0.82 | 0.35 | 0.31 | 0.35 | 0.69 | 0.66 | 0.37 | 0.13 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 186.7 | 0.22 | 0.17 |
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) ) |