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_07 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_07 | 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_07 | 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_07 | 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_07 | dssp | THIS_month:psum | 70.0 | 67 | 75 | 40 | 44 | 74 | 65 | 64.0 | 66.1 | 58.0 | 61 | 4.7 | 0.29 | 0.30 | 0.29 | 0.52 | 0.55 | 0.47 | 87.5 | 10.2 | 5.3 |
sec | 2001_07 | dssp | 1dcj:A | 87.7 | 69 | 100 | 95 | 90 | 94 | 81 | 93.4 | 82 | 100 | 96 | 0.0 | 0.66 | 0.64 | 0.68 | 0.78 | 0.90 | 0.76 | 100.0 | 8.0 | 1.0 |
sec | 2001_07 | dssp | 1e44:B | 68.8 | 9 | 33 | 46 | 82 | 92 | 67 | 42.2 | 10 | 42 | 48 | 1.0 | 0.18 | 0.15 | 0.23 | 0.12 | 0.51 | 0.38 | 100.0 | 8.0 | 13.0 |
sec | 2001_07 | dssp | 1faz:A | 38.5 | 33 | 78 | 0 | 0 | 46 | 39 | 35.9 | 43 | 100 | 28 | 15.5 | 0.02 | 0.03 | 0.02 | 0.19 | 1.0 | 0.04 | 0.0 | 36.0 | 29.0 |
sec | 2001_07 | dssp | 1g7o:A | 74.0 | 82 | 83 | 62 | 37 | 61 | 71 | 74.9 | 79 | 61 | 69 | 3.7 | 0.27 | 0.28 | 0.27 | 0.61 | 0.42 | 0.49 | 100.0 | 0.00 | 5.0 |
sec | 2001_07 | dssp | 1gc5:A | 58.5 | 79 | 61 | 26 | 41 | 47 | 60 | 57.5 | 78 | 27 | 46 | 13.4 | 0.09 | 0.09 | 0.10 | 0.36 | 0.20 | 0.34 | 100.0 | 14.0 | 7.0 |
sec | 2001_07 | dssp | 1h5p:A | 57.9 | 31 | 81 | 40 | 39 | 84 | 60 | 47.8 | 35 | 37 | 56 | 9.4 | 0.13 | 0.13 | 0.15 | 0.40 | 0.21 | 0.38 | 100.0 | 18.0 | 1.0 |
sec | 2001_07 | dssp | 1hq0:A | 62.7 | 55 | 62 | 54 | 62 | 72 | 62 | 59.1 | 59 | 60 | 57 | 6.7 | 0.15 | 0.15 | 0.16 | 0.50 | 0.35 | 0.39 | 100.0 | 2.0 | 4.0 |
sec | 2001_07 | dssp | 1hr6:A | 78.8 | 84 | 81 | 59 | 85 | 80 | 74 | 76.1 | 82 | 68 | 71 | 2.4 | 0.38 | 0.38 | 0.40 | 0.69 | 0.66 | 0.61 | 100.0 | 1.0 | 5.0 |
sec | 2001_07 | dssp | 1hr7:A | 79.0 | 84 | 81 | 60 | 85 | 80 | 74 | 76.6 | 82 | 69 | 72 | 2.4 | 0.38 | 0.38 | 0.40 | 0.69 | 0.67 | 0.61 | 100.0 | 1.0 | 4.0 |
sec | 2001_07 | dssp | 1hr8:A | 79.8 | 90 | 78 | 57 | 88 | 79 | 79 | 76.3 | 87 | 65 | 70 | 2.7 | 0.41 | 0.40 | 0.43 | 0.72 | 0.66 | 0.64 | 100.0 | 6.0 | 6.0 |
sec | 2001_07 | dssp | 1hr9:A | 79.8 | 90 | 77 | 58 | 88 | 78 | 80 | 77.1 | 87 | 66 | 71 | 2.7 | 0.41 | 0.40 | 0.43 | 0.71 | 0.67 | 0.64 | 100.0 | 6.0 | 5.0 |
sec | 2001_07 | dssp | 1hzg:A | 63.1 | 57 | 63 | 54 | 63 | 72 | 62 | 56.9 | 59 | 60 | 53 | 6.1 | 0.16 | 0.16 | 0.16 | 0.51 | 0.36 | 0.38 | 100.0 | 1.0 | 5.0 |
sec | 2001_07 | dssp | 1i3j:A | 58.3 | 22 | 70 | 63 | 25 | 77 | 72 | 48.7 | 25 | 44 | 62 | 12.5 | 0.11 | 0.11 | 0.11 | 0.27 | 0.27 | 0.40 | 100.0 | 21.0 | 17.0 |
sec | 2001_07 | dssp | 1ijx:A | 65.6 | 62 | 79 | 0 | 0 | 80 | 66 | 48.5 | 56 | 0 | 49 | 4.0 | 0.21 | 0.20 | 0.23 | 0.54 | -0.09 | 0.40 | 100.0 | 8.0 | 2.0 |
sec | 2001_07 | dssp | 1ijy:A | 65.6 | 50 | 83 | 28 | 10 | 82 | 72 | 60.3 | 54 | 17 | 69 | 9.0 | 0.19 | 0.20 | 0.18 | 0.48 | 0.08 | 0.49 | 100.0 | 17.0 | 9.0 |
sec | 2001_07 | dssp | 1j8f:A | 71.1 | 73 | 73 | 100 | 83 | 58 | 62 | 75.4 | 79 | 100 | 62 | 0.0 | 0.37 | 0.38 | 0.37 | 0.46 | 0.90 | 0.37 | 100.0 | 0.00 | 2.0 |
sec | 2001_07 | dssp | 1jc5:A | 71.7 | 100 | 56 | 61 | 76 | 68 | 81 | 74.5 | 100 | 65 | 71 | 6.8 | 0.35 | 0.36 | 0.34 | 0.67 | 0.53 | 0.56 | 0.0 | 14.0 | 6.0 |
sec | 2001_07 | dssp | 1jei:A | 73.6 | 90 | 62 | 0 | 0 | 63 | 91 | 69.7 | 88 | 100 | 61 | 0.0 | 0.24 | 0.26 | 0.22 | 0.55 | 1.0 | 0.52 | 100.0 | 16.0 | 1.0 |
sec | 2001_07 | dssp | 1jek:A | 97.5 | 97 | 100 | 0 | 0 | 100 | 66 | 98.8 | 100 | 100 | 75 | 0.0 | 0.66 | 0.76 | 0.57 | 0.80 | 1.0 | 0.80 | 100.0 | 2.0 | 0.00 |
sec | 2001_07 | dssp | 1jek:B | 91.2 | 90 | 100 | 0 | 0 | 100 | 40 | 67.4 | 67 | 100 | 75 | 0.0 | 0.42 | 0.56 | 0.30 | 0.60 | 1.0 | 0.60 | 100.0 | 8.0 | 0.00 |
sec | 2001_07 | dssp | 1jfi:A | 30.0 | 21 | 40 | 0 | 0 | 50 | 27 | 22.5 | 22 | 0 | 25 | 10.0 | 0.12 | 0.13 | 0.12 | -0.34 | -0.04 | -0.14 | 100.0 | 30.0 | 3.0 |
sec | 2001_07 | dssp | 1jfi:B | 82.2 | 81 | 96 | 0 | 0 | 92 | 54 | 79.0 | 81 | 0 | 74 | 0.7 | 0.32 | 0.34 | 0.31 | 0.61 | 1.0 | 0.61 | 100.0 | 12.0 | 1.0 |
sec | 2001_07 | dssp | 1jfy:A | 71.3 | 100 | 76 | 53 | 62 | 50 | 67 | 47.0 | 51 | 48 | 41 | 1.3 | 0.41 | 0.41 | 0.43 | 0.77 | 0.46 | 0.39 | 0.0 | 12.0 | 3.0 |
sec | 2001_07 | dssp | 1jg8:A | 75.5 | 80 | 89 | 61 | 63 | 75 | 66 | 72.2 | 81 | 65 | 63 | 2.6 | 0.35 | 0.36 | 0.36 | 0.72 | 0.54 | 0.53 | 100.0 | 4.0 | 0.00 |
sec | 2001_07 | dssp | THIS_month:psum | 70.0 | 67 | 75 | 40 | 44 | 74 | 65 | 64.0 | 66.1 | 58.0 | 61 | 4.7 | 0.29 | 0.30 | 0.29 | 0.52 | 0.55 | 0.47 | 87.5 | 10.2 | 5.3 |
sec | 2001_07 | 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_07 | 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_07 | 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) ) |