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_11 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_11 | 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_11 | 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_11 | 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_11 | dssp | THIS_month:psum | 71.0 | 65 | 65 | 49 | 47 | 65 | 72 | 66.1 | 68.0 | 69.4 | 60 | 4.0 | 0.01 | -0.02 | 0.05 | 0.55 | 0.60 | 0.46 | 71.8 | 10.4 | 6.3 |
sec | 2000_11 | dssp | 1by6:A | 38.9 | 66 | 16 | 0 | 0 | 33 | 83 | 21.6 | 15 | 100 | 22 | 0.0 | -7.77 | -8.88 | -6.66 | 0.00 | 1.0 | 0.00 | 100.0 | 50.0 | 0.00 |
sec | 2000_11 | dssp | 1c0p:A | 74.1 | 74 | 70 | 59 | 88 | 83 | 70 | 68.2 | 69 | 67 | 68 | 4.1 | 0.34 | 0.33 | 0.35 | 0.60 | 0.64 | 0.57 | 100.0 | 1.0 | 9.0 |
sec | 2000_11 | dssp | 1dfc:A | 66.7 | 0 | 0 | 63 | 76 | 75 | 69 | 64.5 | 0 | 64 | 69 | 3.5 | 0.16 | 0.17 | 0.17 | -0.06 | 0.49 | 0.40 | 100.0 | 3.0 | 7.0 |
sec | 2000_11 | dssp | 1dh3:A | 80.0 | 83 | 93 | 0 | 0 | 57 | 33 | 94.7 | 100 | 100 | 58 | 0.0 | 0.10 | 0.12 | 0.08 | 0.32 | 1.0 | 0.32 | 100.0 | 9.0 | 0.00 |
sec | 2000_11 | dssp | 1dpu:A | 85.5 | 96 | 93 | 33 | 75 | 89 | 78 | 82.3 | 100 | 33 | 77 | 0.0 | 0.60 | 0.57 | 0.64 | 0.91 | 0.45 | 0.71 | 100.0 | 1.0 | 7.0 |
sec | 2000_11 | dssp | 1e0f:I | 75.4 | 0 | 0 | 44 | 30 | 81 | 88 | 56.4 | 100 | 37 | 59 | 0.0 | 0.04 | 0.05 | 0.04 | 1.0 | 0.22 | 0.22 | 100.0 | 0.00 | 7.0 |
sec | 2000_11 | dssp | 1e5d:A | 79.1 | 96 | 77 | 65 | 85 | 69 | 78 | 74.4 | 86 | 67 | 66 | 2.9 | 0.44 | 0.43 | 0.46 | 0.75 | 0.68 | 0.60 | 0.0 | 9.0 | 5.0 |
sec | 2000_11 | dssp | 1e5k:A | 78.7 | 100 | 72 | 67 | 75 | 69 | 88 | 74.7 | 83 | 82 | 67 | 2.6 | 0.46 | 0.46 | 0.46 | 0.77 | 0.63 | 0.63 | 0.0 | 12.0 | 2.0 |
sec | 2000_11 | dssp | 1e79:I | 63.8 | 100 | 48 | 100 | 60 | 43 | 100 | 47.2 | 100 | 80 | 32 | 0.0 | 0.37 | 0.39 | 0.36 | 0.51 | 0.75 | 0.46 | 100.0 | 31.0 | 4.0 |
sec | 2000_11 | dssp | 1e96:B | 71.7 | 85 | 77 | 33 | 18 | 45 | 66 | 54.7 | 61 | 25 | 45 | 4.3 | 0.12 | 0.12 | 0.13 | 0.40 | 0.21 | 0.40 | 0.0 | 7.0 | 2.0 |
sec | 2000_11 | dssp | 1ehx:A | 74.5 | 50 | 85 | 85 | 63 | 72 | 85 | 79.3 | 50 | 74 | 90 | 5.3 | 0.32 | 0.31 | 0.33 | 0.62 | 0.54 | 0.60 | 100.0 | 5.0 | 12.0 |
sec | 2000_11 | dssp | 1ev0:A | 65.5 | 66 | 73 | 72 | 68 | 57 | 55 | 69.1 | 71 | 84 | 51 | 5.1 | 0.26 | 0.26 | 0.26 | 0.54 | 0.56 | 0.34 | 100.0 | 3.0 | 1.0 |
sec | 2000_11 | dssp | 1f2n:A | 61.9 | 25 | 38 | 71 | 59 | 66 | 68 | 56.2 | 22 | 65 | 58 | 5.8 | 0.14 | 0.14 | 0.15 | 0.21 | 0.43 | 0.35 | 100.0 | 5.0 | 6.0 |
sec | 2000_11 | dssp | 1f5m:A | 75.0 | 80 | 87 | 55 | 60 | 81 | 72 | 79.9 | 83 | 65 | 85 | 6.8 | 0.36 | 0.37 | 0.37 | 0.74 | 0.44 | 0.62 | 100.0 | 2.0 | 1.0 |
sec | 2000_11 | dssp | 1faf:A | 83.5 | 91 | 83 | 0 | 0 | 70 | 84 | 79.8 | 93 | 100 | 62 | 0.0 | 0.33 | 0.33 | 0.35 | 0.64 | 1.0 | 0.64 | 100.0 | 6.0 | 0.00 |
sec | 2000_11 | dssp | 1fd3:A | 75.6 | 0 | 0 | 84 | 73 | 90 | 76 | 77.0 | 0 | 92 | 88 | 4.8 | 0.33 | 0.27 | 0.40 | 1.0 | 0.67 | 0.61 | 100.0 | 14.0 | 4.0 |
sec | 2000_11 | dssp | 1fi2:A | 74.1 | 29 | 100 | 73 | 64 | 88 | 77 | 59.0 | 29 | 74 | 59 | 5.9 | 0.30 | 0.27 | 0.33 | 0.50 | 0.54 | 0.60 | 100.0 | 11.0 | 3.0 |
sec | 2000_11 | dssp | 1fp3:A | 71.9 | 86 | 79 | 35 | 37 | 57 | 65 | 63.7 | 77 | 20 | 52 | 4.4 | 0.21 | 0.21 | 0.22 | 0.57 | 0.30 | 0.44 | 100.0 | 4.0 | 0.00 |
sec | 2000_11 | dssp | 1fs1:A | 75.6 | 88 | 76 | 0 | 0 | 53 | 72 | 62.4 | 64 | 100 | 59 | 0.0 | 0.16 | 0.15 | 0.17 | 0.45 | 1.0 | 0.45 | 100.0 | 9.0 | 0.00 |
sec | 2000_11 | dssp | 1fsi:A | 61.3 | 97 | 51 | 41 | 80 | 48 | 72 | 56.5 | 85 | 31 | 55 | 15.3 | 0.23 | 0.21 | 0.25 | 0.52 | 0.44 | 0.44 | 0.0 | 27.0 | 17.0 |
sec | 2000_11 | dssp | 1fuk:A | 78.3 | 89 | 75 | 88 | 75 | 62 | 85 | 85.3 | 91 | 91 | 76 | 1.9 | 0.43 | 0.43 | 0.43 | 0.70 | 0.76 | 0.58 | 100.0 | 7.0 | 3.0 |
sec | 2000_11 | dssp | 1fvi:A | 48.8 | 45 | 33 | 9 | 33 | 71 | 60 | 45.0 | 50 | 13 | 58 | 13.9 | 0.04 | 0.04 | 0.05 | 0.13 | 0.04 | 0.26 | 100.0 | 9.0 | 18.0 |
sec | 2000_11 | dssp | 1fx8:A | 66.9 | 59 | 96 | 0 | 0 | 89 | 61 | 70.4 | 69 | 100 | 73 | 15.7 | 0.28 | 0.36 | 0.20 | 0.46 | 1.0 | 0.62 | 0.0 | 28.0 | 16.0 |
sec | 2000_11 | dssp | 1fy7:A | 74.4 | 80 | 80 | 62 | 79 | 76 | 67 | 73.9 | 87 | 72 | 63 | 1.8 | 0.35 | 0.34 | 0.36 | 0.69 | 0.62 | 0.51 | 0.0 | 0.00 | 5.0 |
sec | 2000_11 | dssp | 1fyx:A | 63.8 | 82 | 60 | 52 | 80 | 46 | 64 | 60.9 | 68 | 67 | 50 | 5.3 | 0.18 | 0.17 | 0.20 | 0.38 | 0.59 | 0.32 | 100.0 | 16.0 | 5.0 |
sec | 2000_11 | dssp | 1g1p:A | 62.5 | 0 | 0 | 71 | 33 | 60 | 88 | 49.2 | 100 | 30 | 53 | 0.0 | 0.05 | 0.07 | 0.05 | 1.0 | 0.26 | 0.26 | 100.0 | 0.00 | 25.0 |
sec | 2000_11 | dssp | 1g25:A | 73.8 | 30 | 100 | 87 | 36 | 84 | 88 | 73.1 | 46 | 68 | 81 | 7.6 | 0.30 | 0.30 | 0.31 | 0.51 | 0.47 | 0.58 | 100.0 | 13.0 | 16.0 |
sec | 2000_11 | dssp | 1g2i:A | 71.7 | 57 | 100 | 85 | 66 | 77 | 60 | 69.2 | 69 | 83 | 59 | 3.0 | 0.39 | 0.39 | 0.40 | 0.67 | 0.66 | 0.48 | 0.0 | 16.0 | 7.0 |
sec | 2000_11 | dssp | 1g5t:A | 72.6 | 75 | 77 | 75 | 60 | 68 | 74 | 81.3 | 84 | 81 | 78 | 5.0 | 0.28 | 0.29 | 0.28 | 0.60 | 0.58 | 0.53 | 0.0 | 1.0 | 4.0 |
sec | 2000_11 | dssp | 1g61:A | 65.8 | 65 | 100 | 79 | 49 | 56 | 65 | 62.0 | 78 | 57 | 50 | 5.7 | 0.33 | 0.33 | 0.34 | 0.74 | 0.43 | 0.38 | 0.0 | 11.0 | 16.0 |
sec | 2000_11 | dssp | 1g7d:A | 75.5 | 94 | 74 | 0 | 0 | 40 | 78 | 64.3 | 83 | 100 | 36 | 0.0 | 0.16 | 0.14 | 0.19 | 0.43 | 1.0 | 0.43 | 100.0 | 16.0 | 0.00 |
sec | 2000_11 | dssp | 1qoj:A | 86.7 | 97 | 88 | 0 | 0 | 28 | 66 | 59.0 | 65 | 100 | 21 | 0.0 | 0.15 | 0.11 | 0.20 | 0.37 | 1.0 | 0.37 | 100.0 | 8.0 | 0.00 |
sec | 2000_11 | dssp | THIS_month:psum | 71.0 | 65 | 65 | 49 | 47 | 65 | 72 | 66.1 | 68.0 | 69.4 | 60 | 4.0 | 0.01 | -0.02 | 0.05 | 0.55 | 0.60 | 0.46 | 71.8 | 10.4 | 6.3 |
sec | 2000_11 | 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_11 | 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_11 | 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) ) |