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 2002_03 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_03 | 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 | 2002_03 | 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 | 2002_03 | 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 | 2002_03 | dssp | THIS_month:psum | 71.9 | 57 | 60 | 56 | 59 | 76 | 69 | 70.4 | 60.5 | 73.0 | 67.9 | 5.5 | 0.33 | 0.33 | 0.33 | 0.56 | 0.56 | 0.53 | 84.6 | 7.9 | 7.3 |
sec | 2002_03 | dssp | 1gk7:A | 92.3 | 94 | 97 | 0 | 0 | 75 | 60 | 98.3 | 100 | 100 | 83 | 0.0 | 0.36 | 0.39 | 0.34 | 0.62 | 1.0 | 0.62 | 100.0 | 2.0 | 0.00 |
sec | 2002_03 | dssp | 1i60:A | 71.6 | 75 | 80 | 66 | 62 | 69 | 65 | 69.9 | 75 | 70 | 61 | 4.6 | 0.26 | 0.27 | 0.27 | 0.60 | 0.56 | 0.48 | 100.0 | 3.0 | 1.0 |
sec | 2002_03 | dssp | 1ib8:A | 80.5 | 92 | 72 | 85 | 84 | 69 | 82 | 90.4 | 100 | 96 | 80 | 0.6 | 0.48 | 0.49 | 0.48 | 0.75 | 0.77 | 0.60 | 100.0 | 6.0 | 0.00 |
sec | 2002_03 | dssp | 1j4w:A | 75.7 | 58 | 100 | 90 | 86 | 100 | 48 | 84.3 | 76 | 100 | 81 | 4.0 | 0.51 | 0.54 | 0.49 | 0.63 | 0.83 | 0.60 | 100.0 | 21.0 | 1.0 |
sec | 2002_03 | dssp | 1j5b:A | 97.3 | 97 | 100 | 0 | 0 | 100 | 66 | 98.6 | 100 | 100 | 75 | 0.0 | 0.65 | 0.75 | 0.56 | 0.80 | 1.0 | 0.80 | 100.0 | 2.0 | 0.00 |
sec | 2002_03 | dssp | 1j8c:A | 89.3 | 93 | 82 | 77 | 95 | 93 | 89 | 92.9 | 100 | 88 | 92 | 0.0 | 0.62 | 0.62 | 0.63 | 0.85 | 0.82 | 0.77 | 100.0 | 1.0 | 4.0 |
sec | 2002_03 | dssp | 1jjg:A | 70.6 | 100 | 50 | 90 | 58 | 57 | 92 | 42.3 | 75 | 96 | 30 | 0.0 | 0.34 | 0.37 | 0.31 | 0.68 | 0.56 | 0.49 | 100.0 | 5.0 | 17.0 |
sec | 2002_03 | dssp | 1jmk:O | 79.1 | 87 | 78 | 72 | 65 | 74 | 89 | 81.3 | 88 | 81 | 75 | 6.9 | 0.42 | 0.42 | 0.42 | 0.70 | 0.60 | 0.71 | 0.0 | 4.0 | 2.0 |
sec | 2002_03 | dssp | 1jmr:B | 78.9 | 84 | 88 | 69 | 72 | 77 | 70 | 78.0 | 87 | 80 | 66 | 2.4 | 0.41 | 0.41 | 0.41 | 0.75 | 0.63 | 0.59 | 100.0 | 2.0 | 0.00 |
sec | 2002_03 | dssp | 1jo8:A | 72.4 | 0 | 0 | 76 | 74 | 75 | 70 | 72.3 | 0 | 76 | 75 | 0.0 | 0.22 | 0.20 | 0.25 | 1.0 | 0.54 | 0.44 | 100.0 | 5.0 | 1.0 |
sec | 2002_03 | dssp | 1k11:A | 20.4 | 22 | 6 | 8 | 25 | 37 | 52 | 22.9 | 14 | 12 | 48 | 47.9 | 0.20 | 0.20 | 0.21 | -0.36 | -0.21 | 0.23 | 100.0 | 41.0 | 32.0 |
sec | 2002_03 | dssp | 1k24:A | 45.8 | 0 | 0 | 29 | 94 | 84 | 36 | 36.6 | 0 | 29 | 61 | 5.2 | 0.07 | 0.08 | 0.07 | -0.03 | 0.29 | 0.20 | 0.0 | 7.0 | 46.0 |
sec | 2002_03 | dssp | 1k8h:A | 64.7 | 77 | 42 | 48 | 81 | 70 | 76 | 70.4 | 74 | 56 | 79 | 12.0 | 0.23 | 0.24 | 0.24 | 0.41 | 0.50 | 0.52 | 100.0 | 17.0 | 13.0 |
sec | 2002_03 | dssp | 1kg0:C | 73.5 | 86 | 76 | 81 | 52 | 68 | 88 | 68.3 | 96 | 62 | 66 | 0.0 | 0.35 | 0.38 | 0.34 | 0.78 | 0.51 | 0.49 | 100.0 | 1.0 | 13.0 |
sec | 2002_03 | dssp | 1kil:E | 92.7 | 94 | 97 | 0 | 0 | 80 | 66 | 98.8 | 100 | 100 | 90 | 0.0 | 0.42 | 0.45 | 0.40 | 0.68 | 1.0 | 0.68 | 100.0 | 2.0 | 0.00 |
sec | 2002_03 | dssp | 1kj6:A | 73.3 | 0 | 0 | 69 | 75 | 88 | 72 | 74.4 | 0 | 81 | 84 | 0.0 | 0.27 | 0.21 | 0.33 | 1.0 | 0.61 | 0.43 | 100.0 | 11.0 | 2.0 |
sec | 2002_03 | dssp | 1kjk:A | 67.3 | 41 | 100 | 50 | 60 | 100 | 62 | 65.0 | 58 | 58 | 74 | 8.1 | 0.34 | 0.31 | 0.38 | 0.56 | 0.41 | 0.60 | 100.0 | 20.0 | 4.0 |
sec | 2002_03 | dssp | 1kl9:A | 62.0 | 0 | 0 | 66 | 58 | 65 | 85 | 50.8 | 0 | 82 | 41 | 14.0 | 0.19 | 0.20 | 0.18 | -0.09 | 0.31 | 0.53 | 100.0 | 6.0 | 6.0 |
sec | 2002_03 | dssp | 1kqf:B | 68.2 | 37 | 86 | 45 | 54 | 93 | 67 | 57.9 | 52 | 53 | 62 | 5.8 | 0.22 | 0.20 | 0.26 | 0.47 | 0.39 | 0.51 | 100.0 | 16.0 | 3.0 |
sec | 2002_03 | dssp | 1kqf:C | 75.0 | 78 | 90 | 42 | 16 | 66 | 54 | 75.3 | 79 | 46 | 61 | 6.4 | 0.17 | 0.20 | 0.15 | 0.46 | 0.22 | 0.48 | 0.0 | 9.0 | 5.0 |
sec | 2002_03 | dssp | 1kqr:A | 68.8 | 50 | 100 | 71 | 79 | 70 | 53 | 72.8 | 75 | 76 | 66 | 0.6 | 0.25 | 0.24 | 0.26 | 0.68 | 0.46 | 0.37 | 100.0 | 5.0 | 5.0 |
sec | 2002_03 | dssp | 1ktb:A | 70.4 | 67 | 75 | 54 | 79 | 80 | 65 | 68.8 | 73 | 65 | 67 | 1.8 | 0.28 | 0.27 | 0.30 | 0.59 | 0.57 | 0.46 | 0.0 | 3.0 | 7.0 |
sec | 2002_03 | dssp | 1kvk:A | 50.7 | 0 | 0 | 50 | 76 | 70 | 51 | 45.8 | 0 | 50 | 52 | 17.8 | 0.13 | 0.14 | 0.13 | -0.18 | 0.33 | 0.36 | 100.0 | 6.0 | 19.0 |
sec | 2002_03 | dssp | 1kvv:A | 91.3 | 90 | 96 | 83 | 76 | 93 | 91 | 97.1 | 100 | 91 | 96 | 0.0 | 0.66 | 0.67 | 0.66 | 0.90 | 0.77 | 0.82 | 100.0 | 1.0 | 0.00 |
sec | 2002_03 | dssp | 1kzy:C | 57.3 | 61 | 50 | 51 | 48 | 56 | 66 | 46.2 | 51 | 51 | 41 | 5.6 | 0.11 | 0.12 | 0.12 | 0.33 | 0.38 | 0.26 | 100.0 | 6.0 | 0.00 |
sec | 2002_03 | dssp | 1l1c:A | 81.8 | 0 | 0 | 95 | 77 | 80 | 85 | 71.2 | 0 | 100 | 61 | 0.0 | 0.45 | 0.40 | 0.50 | 1.0 | 0.75 | 0.63 | 100.0 | 5.0 | 9.0 |
sec | 2002_03 | dssp | THIS_month:psum | 71.9 | 57 | 60 | 56 | 59 | 76 | 69 | 70.4 | 60.5 | 73.0 | 67.9 | 5.5 | 0.33 | 0.33 | 0.33 | 0.56 | 0.56 | 0.53 | 84.6 | 7.9 | 7.3 |
sec | 2002_03 | 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 | 2002_03 | 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 | 2002_03 | 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) ) |