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 2000_12 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 | 2000_12 | 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 | 2000_12 | 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 | 2000_12 | 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 | 2000_12 | dssp | THIS_month:psum | 73.5 | 67 | 69 | 50 | 53 | 72 | 68 | 69.1 | 72.5 | 67.4 | 64.1 | 3.3 | 0.31 | 0.30 | 0.31 | 0.63 | 0.61 | 0.49 | 75.6 | 6.6 | 5.1 |
sec | 2000_12 | dssp | 1ci6:A | 96.4 | 96 | 100 | 0 | 0 | 100 | 60 | 99.1 | 100 | 100 | 83 | 0.0 | 0.60 | 0.71 | 0.49 | 0.75 | 1.0 | 0.75 | 100.0 | 3.0 | 0.00 |
sec | 2000_12 | dssp | 1ci6:B | 91.5 | 93 | 97 | 0 | 0 | 75 | 50 | 98.4 | 100 | 100 | 81 | 0.0 | 0.31 | 0.35 | 0.27 | 0.56 | 1.0 | 0.56 | 100.0 | 4.0 | 0.00 |
sec | 2000_12 | dssp | 1d2t:A | 73.1 | 66 | 85 | 0 | 0 | 80 | 70 | 59.9 | 57 | 100 | 62 | 2.2 | 0.21 | 0.23 | 0.19 | 0.54 | 1.0 | 0.51 | 0.0 | 11.0 | 5.0 |
sec | 2000_12 | dssp | 1d7y:A | 75.6 | 80 | 78 | 71 | 78 | 75 | 71 | 72.4 | 85 | 72 | 64 | 1.7 | 0.36 | 0.37 | 0.37 | 0.71 | 0.64 | 0.53 | 100.0 | 0.00 | 2.0 |
sec | 2000_12 | dssp | 1dkc:A | 75.7 | 0 | 0 | 53 | 70 | 87 | 77 | 57.4 | 100 | 69 | 53 | 0.0 | 0.15 | 0.15 | 0.17 | 1.0 | 0.44 | 0.44 | 100.0 | 0.00 | 8.0 |
sec | 2000_12 | dssp | 1dl5:A | 63.4 | 68 | 76 | 45 | 60 | 74 | 55 | 59.8 | 70 | 51 | 57 | 8.2 | 0.19 | 0.19 | 0.20 | 0.58 | 0.35 | 0.42 | 100.0 | 3.0 | 7.0 |
sec | 2000_12 | dssp | 1dl9:A | 59.7 | 50 | 34 | 46 | 24 | 63 | 83 | 53.4 | 51 | 36 | 54 | 5.3 | 0.08 | 0.10 | 0.07 | 0.19 | 0.27 | 0.29 | 100.0 | 11.0 | 5.0 |
sec | 2000_12 | dssp | 1dmg:A | 64.3 | 75 | 75 | 63 | 70 | 53 | 50 | 66.1 | 75 | 79 | 46 | 0.0 | 0.30 | 0.30 | 0.31 | 0.59 | 0.55 | 0.23 | 100.0 | 0.00 | 2.0 |
sec | 2000_12 | dssp | 1e2x:A | 77.5 | 80 | 93 | 60 | 54 | 70 | 46 | 71.5 | 73 | 65 | 64 | 0.9 | 0.27 | 0.29 | 0.25 | 0.55 | 0.55 | 0.44 | 100.0 | 10.0 | 0.00 |
sec | 2000_12 | dssp | 1edz:A | 75.7 | 77 | 91 | 56 | 69 | 82 | 67 | 71.5 | 92 | 62 | 59 | 0.3 | 0.39 | 0.38 | 0.40 | 0.75 | 0.55 | 0.53 | 100.0 | 5.0 | 3.0 |
sec | 2000_12 | dssp | 1ekt:A | 88.7 | 100 | 77 | 80 | 92 | 90 | 90 | 99.1 | 100 | 100 | 98 | 0.0 | 0.62 | 0.64 | 0.62 | 0.86 | 0.81 | 0.76 | 100.0 | 3.0 | 3.0 |
sec | 2000_12 | dssp | 1eo1:A | 80.6 | 92 | 75 | 81 | 70 | 76 | 88 | 79.2 | 100 | 86 | 71 | 0.0 | 0.46 | 0.48 | 0.45 | 0.78 | 0.68 | 0.62 | 100.0 | 4.0 | 3.0 |
sec | 2000_12 | dssp | 1ewn:A | 68.8 | 44 | 67 | 70 | 71 | 79 | 67 | 50.3 | 42 | 66 | 45 | 3.5 | 0.25 | 0.24 | 0.26 | 0.44 | 0.59 | 0.45 | 100.0 | 8.0 | 0.00 |
sec | 2000_12 | dssp | 1f2d:A | 79.8 | 81 | 86 | 80 | 72 | 78 | 75 | 82.4 | 86 | 87 | 76 | 0.8 | 0.43 | 0.44 | 0.43 | 0.72 | 0.71 | 0.60 | 100.0 | 2.0 | 1.0 |
sec | 2000_12 | dssp | 1f53:A | 73.8 | 0 | 0 | 71 | 63 | 75 | 81 | 72.5 | 100 | 69 | 74 | 0.0 | 0.16 | 0.16 | 0.16 | 1.0 | 0.45 | 0.45 | 100.0 | 0.00 | 4.0 |
sec | 2000_12 | dssp | 1f5q:B | 66.4 | 68 | 87 | 0 | 0 | 60 | 61 | 70.0 | 71 | 100 | 65 | 12.1 | 0.14 | 0.18 | 0.11 | 0.38 | 1.0 | 0.46 | 0.0 | 15.0 | 15.0 |
sec | 2000_12 | dssp | 1f62:A | 74.5 | 0 | 0 | 75 | 21 | 81 | 94 | 58.6 | 0 | 46 | 62 | 5.8 | 0.16 | 0.17 | 0.16 | 1.0 | 0.31 | 0.45 | 100.0 | 7.0 | 19.0 |
sec | 2000_12 | dssp | 1f6d:A | 81.4 | 80 | 90 | 80 | 82 | 83 | 71 | 78.8 | 81 | 76 | 76 | 0.5 | 0.47 | 0.47 | 0.47 | 0.73 | 0.78 | 0.62 | 100.0 | 5.0 | 0.00 |
sec | 2000_12 | dssp | 1f7c:A | 81.3 | 80 | 95 | 0 | 0 | 83 | 69 | 81.0 | 88 | 100 | 68 | 1.0 | 0.36 | 0.41 | 0.31 | 0.68 | 1.0 | 0.62 | 100.0 | 10.0 | 3.0 |
sec | 2000_12 | dssp | 1fjn:A | 53.8 | 0 | 0 | 50 | 50 | 80 | 54 | 22.4 | 0 | 37 | 27 | 0.0 | 0.15 | 0.10 | 0.20 | 1.0 | 0.37 | 0.03 | 100.0 | 25.0 | 0.00 |
sec | 2000_12 | dssp | 1fou:A | 62.3 | 56 | 64 | 55 | 42 | 68 | 66 | 56.0 | 57 | 62 | 54 | 3.9 | 0.13 | 0.13 | 0.13 | 0.39 | 0.40 | 0.32 | 100.0 | 4.0 | 3.0 |
sec | 2000_12 | dssp | 1fpo:A | 84.2 | 93 | 87 | 0 | 0 | 56 | 86 | 77.3 | 78 | 100 | 73 | 2.3 | 0.30 | 0.32 | 0.30 | 0.59 | 1.0 | 0.62 | 100.0 | 5.0 | 3.0 |
sec | 2000_12 | dssp | 1fr3:A | 79.1 | 60 | 100 | 86 | 84 | 73 | 63 | 75.8 | 70 | 74 | 81 | 1.4 | 0.40 | 0.39 | 0.42 | 0.74 | 0.66 | 0.54 | 100.0 | 5.0 | 1.0 |
sec | 2000_12 | dssp | 1fu1:A | 57.9 | 100 | 58 | 1 | 100 | 50 | 56 | 49.1 | 82 | 1 | 46 | 19.1 | 0.23 | 0.17 | 0.31 | 0.49 | 0.11 | 0.37 | 0.0 | 32.0 | 29.0 |
sec | 2000_12 | dssp | 1fwk:A | 78.4 | 88 | 79 | 64 | 91 | 78 | 70 | 85.3 | 92 | 81 | 80 | 2.7 | 0.43 | 0.42 | 0.44 | 0.73 | 0.69 | 0.59 | 0.0 | 4.0 | 8.0 |
sec | 2000_12 | dssp | 1fx3:A | 70.6 | 77 | 94 | 65 | 70 | 68 | 55 | 76.2 | 94 | 68 | 67 | 0.0 | 0.40 | 0.40 | 0.41 | 0.79 | 0.53 | 0.38 | 0.0 | 6.0 | 2.0 |
sec | 2000_12 | dssp | 1fxk:B | 80.7 | 100 | 79 | 0 | 0 | 31 | 100 | 51.0 | 59 | 0 | 37 | 9.1 | 0.32 | 0.13 | 0.51 | 0.39 | 1.0 | 0.52 | 0.0 | 19.0 | 9.0 |
sec | 2000_12 | dssp | 1fxo:A | 78.4 | 82 | 83 | 79 | 78 | 73 | 73 | 83.0 | 88 | 89 | 74 | 1.0 | 0.42 | 0.43 | 0.43 | 0.73 | 0.72 | 0.56 | 100.0 | 0.00 | 0.00 |
sec | 2000_12 | dssp | 1fxx:A | 73.7 | 75 | 72 | 38 | 76 | 90 | 74 | 76.7 | 82 | 47 | 86 | 7.6 | 0.32 | 0.30 | 0.34 | 0.60 | 0.46 | 0.64 | 0.0 | 1.0 | 10.0 |
sec | 2000_12 | dssp | 1g6g:A | 63.8 | 20 | 20 | 79 | 66 | 62 | 72 | 66.3 | 26 | 80 | 65 | 5.5 | 0.16 | 0.17 | 0.17 | 0.09 | 0.53 | 0.39 | 100.0 | 0.00 | 7.0 |
sec | 2000_12 | dssp | 1g7t:A | 91.2 | 100 | 100 | 75 | 85 | 92 | 85 | 88.7 | 100 | 75 | 85 | 0.0 | 0.77 | 0.76 | 0.78 | 1.0 | 0.74 | 0.81 | 100.0 | 0.00 | 2.0 |
sec | 2000_12 | dssp | 1g8k:A | 63.6 | 59 | 72 | 38 | 50 | 76 | 62 | 52.1 | 55 | 43 | 52 | 4.3 | 0.15 | 0.15 | 0.17 | 0.50 | 0.33 | 0.37 | 100.0 | 6.0 | 4.0 |
sec | 2000_12 | dssp | 1g99:A | 74.1 | 78 | 79 | 60 | 71 | 76 | 69 | 71.1 | 79 | 66 | 65 | 4.2 | 0.31 | 0.31 | 0.32 | 0.63 | 0.58 | 0.55 | 100.0 | 0.00 | 3.0 |
sec | 2000_12 | dssp | 1ga6:A | 59.1 | 46 | 69 | 52 | 50 | 73 | 59 | 56.5 | 55 | 54 | 58 | 10.0 | 0.12 | 0.12 | 0.13 | 0.41 | 0.33 | 0.38 | 0.0 | 10.0 | 0.00 |
sec | 2000_12 | dssp | 1gak:A | 59.9 | 64 | 79 | 50 | 5 | 47 | 43 | 43.7 | 45 | 5 | 37 | 10.2 | 0.06 | 0.07 | 0.05 | 0.18 | 0.13 | 0.24 | 0.0 | 13.0 | 10.0 |
sec | 2000_12 | dssp | 1gg4:A | 76.2 | 89 | 74 | 75 | 73 | 67 | 79 | 78.0 | 90 | 75 | 70 | 0.5 | 0.40 | 0.41 | 0.40 | 0.72 | 0.67 | 0.53 | 100.0 | 6.0 | 0.00 |
sec | 2000_12 | dssp | 1ggx:A | 67.7 | 88 | 53 | 58 | 100 | 72 | 53 | 69.1 | 63 | 76 | 60 | 1.5 | 0.39 | 0.41 | 0.38 | 0.62 | 0.63 | 0.38 | 100.0 | 9.0 | 21.0 |
sec | 2000_12 | dssp | THIS_month:psum | 73.5 | 67 | 69 | 50 | 53 | 72 | 68 | 69.1 | 72.5 | 67.4 | 64.1 | 3.3 | 0.31 | 0.30 | 0.31 | 0.63 | 0.61 | 0.49 | 75.6 | 6.6 | 5.1 |
sec | 2000_12 | 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 | 2000_12 | 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 | 2000_12 | 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) ) |