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_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 | 2001_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 | 2001_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 | 2001_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 | 2001_03 | dssp | THIS_month:psum | 70.9 | 70 | 70 | 48 | 41 | 66 | 69 | 65.0 | 70.1 | 59.0 | 58.9 | 4.0 | 0.25 | 0.25 | 0.25 | 0.57 | 0.56 | 0.45 | 85.7 | 6.9 | 5.2 |
sec | 2001_03 | dssp | 1ejj:A | 75.4 | 72 | 79 | 70 | 66 | 79 | 75 | 70.8 | 70 | 77 | 68 | 3.7 | 0.32 | 0.32 | 0.32 | 0.62 | 0.61 | 0.58 | 100.0 | 3.0 | 0.00 |
sec | 2001_03 | dssp | 1ekp:A | 80.5 | 83 | 81 | 73 | 78 | 83 | 81 | 73.6 | 85 | 72 | 69 | 2.7 | 0.43 | 0.43 | 0.43 | 0.77 | 0.65 | 0.66 | 100.0 | 0.00 | 1.0 |
sec | 2001_03 | dssp | 1eu8:A | 70.8 | 68 | 84 | 68 | 61 | 74 | 62 | 73.1 | 77 | 68 | 69 | 4.9 | 0.27 | 0.27 | 0.27 | 0.59 | 0.56 | 0.49 | 100.0 | 8.0 | 2.0 |
sec | 2001_03 | dssp | 1eum:A | 81.4 | 88 | 93 | 0 | 0 | 56 | 62 | 72.9 | 76 | 0 | 61 | 3.1 | 0.27 | 0.31 | 0.23 | 0.59 | -0.02 | 0.49 | 0.0 | 4.0 | 6.0 |
sec | 2001_03 | dssp | 1f75:A | 76.7 | 82 | 80 | 50 | 85 | 80 | 68 | 79.9 | 86 | 64 | 75 | 6.8 | 0.35 | 0.34 | 0.37 | 0.58 | 0.60 | 0.62 | 100.0 | 1.0 | 6.0 |
sec | 2001_03 | dssp | 1fi4:A | 68.3 | 74 | 72 | 45 | 65 | 74 | 65 | 59.0 | 63 | 54 | 56 | 5.8 | 0.21 | 0.21 | 0.23 | 0.55 | 0.45 | 0.47 | 100.0 | 1.0 | 6.0 |
sec | 2001_03 | dssp | 1fn9:A | 56.4 | 43 | 82 | 52 | 28 | 70 | 57 | 50.9 | 57 | 45 | 47 | 6.8 | 0.11 | 0.12 | 0.12 | 0.43 | 0.26 | 0.27 | 100.0 | 20.0 | 10.0 |
sec | 2001_03 | dssp | 1fp1:D | 74.8 | 81 | 78 | 46 | 58 | 71 | 72 | 64.9 | 62 | 53 | 72 | 5.6 | 0.25 | 0.24 | 0.26 | 0.54 | 0.47 | 0.57 | 100.0 | 2.0 | 1.0 |
sec | 2001_03 | dssp | 1fpx:A | 64.6 | 61 | 80 | 65 | 55 | 68 | 53 | 63.6 | 66 | 71 | 55 | 7.2 | 0.18 | 0.19 | 0.18 | 0.46 | 0.51 | 0.39 | 100.0 | 12.0 | 3.0 |
sec | 2001_03 | dssp | 1fse:A | 95.5 | 97 | 95 | 0 | 0 | 91 | 95 | 100.0 | 100 | 100 | 100 | 0.0 | 0.72 | 0.72 | 0.73 | 0.90 | 1.0 | 0.90 | 100.0 | 1.0 | 0.00 |
sec | 2001_03 | dssp | 1fw9:A | 54.3 | 65 | 44 | 31 | 71 | 70 | 55 | 46.4 | 51 | 31 | 63 | 14.0 | 0.10 | 0.10 | 0.11 | 0.34 | 0.30 | 0.36 | 100.0 | 11.0 | 21.0 |
sec | 2001_03 | dssp | 1g12:A | 64.7 | 54 | 96 | 69 | 28 | 79 | 58 | 60.5 | 60 | 57 | 62 | 7.7 | 0.23 | 0.25 | 0.22 | 0.55 | 0.36 | 0.46 | 100.0 | 24.0 | 11.0 |
sec | 2001_03 | dssp | 1g2h:A | 73.8 | 100 | 63 | 0 | 0 | 51 | 100 | 76.9 | 88 | 100 | 66 | 0.0 | 0.34 | 0.31 | 0.37 | 0.57 | 1.0 | 0.57 | 0.0 | 26.0 | 0.00 |
sec | 2001_03 | dssp | 1g5b:A | 66.7 | 60 | 75 | 75 | 52 | 67 | 70 | 67.9 | 64 | 76 | 66 | 5.4 | 0.22 | 0.22 | 0.22 | 0.53 | 0.51 | 0.43 | 100.0 | 6.0 | 8.0 |
sec | 2001_03 | dssp | 1g5h:A | 66.2 | 63 | 84 | 33 | 25 | 78 | 60 | 57.3 | 64 | 33 | 52 | 6.7 | 0.20 | 0.21 | 0.20 | 0.51 | 0.20 | 0.46 | 100.0 | 13.0 | 3.0 |
sec | 2001_03 | dssp | 1g8e:A | 83.7 | 94 | 87 | 100 | 37 | 55 | 88 | 75.0 | 78 | 66 | 68 | 2.0 | 0.39 | 0.40 | 0.39 | 0.67 | 0.59 | 0.62 | 0.0 | 5.0 | 5.0 |
sec | 2001_03 | dssp | 1g9l:A | 73.6 | 78 | 49 | 0 | 0 | 71 | 90 | 63.1 | 77 | 100 | 59 | 0.0 | 0.16 | 0.18 | 0.15 | 0.44 | 1.0 | 0.44 | 100.0 | 15.0 | 0.00 |
sec | 2001_03 | dssp | 1gef:A | 77.5 | 76 | 91 | 82 | 80 | 73 | 63 | 82.7 | 77 | 95 | 74 | 0.8 | 0.44 | 0.44 | 0.45 | 0.76 | 0.71 | 0.52 | 0.0 | 5.0 | 0.00 |
sec | 2001_03 | dssp | 1ggq:A | 84.0 | 97 | 85 | 0 | 0 | 61 | 77 | 82.0 | 97 | 0 | 53 | 2.4 | 0.35 | 0.28 | 0.42 | 0.65 | 1.0 | 0.60 | 100.0 | 9.0 | 4.0 |
sec | 2001_03 | dssp | 1gh5:A | 71.3 | 0 | 0 | 69 | 70 | 73 | 71 | 70.4 | 100 | 76 | 64 | 0.0 | 0.13 | 0.13 | 0.13 | 1.0 | 0.42 | 0.42 | 100.0 | 0.00 | 1.0 |
sec | 2001_03 | dssp | 1hg3:A | 86.2 | 90 | 91 | 87 | 72 | 81 | 87 | 83.1 | 92 | 88 | 73 | 1.7 | 0.55 | 0.56 | 0.54 | 0.84 | 0.74 | 0.74 | 100.0 | 0.00 | 3.0 |
sec | 2001_03 | dssp | 1hhn:A | 84.2 | 0 | 0 | 0 | 0 | 100 | 84 | 14.8 | 0 | 0 | 17 | 0.0 | 0.00 | 0.00 | 0.00 | 1.0 | 1.0 | 0.00 | 100.0 | 3.0 | 11.0 |
sec | 2001_03 | dssp | 1hn5:A | 58.1 | 77 | 66 | 36 | 43 | 41 | 48 | 53.5 | 66 | 40 | 42 | 5.4 | 0.12 | 0.12 | 0.13 | 0.42 | 0.29 | 0.17 | 100.0 | 7.0 | 2.0 |
sec | 2001_03 | dssp | 1hn5:B | 54.5 | 67 | 63 | 51 | 34 | 43 | 53 | 47.3 | 54 | 51 | 38 | 2.2 | 0.14 | 0.15 | 0.14 | 0.39 | 0.32 | 0.11 | 100.0 | 2.0 | 6.0 |
sec | 2001_03 | dssp | 1hn5:C | 72.6 | 73 | 89 | 87 | 48 | 67 | 63 | 70.0 | 71 | 89 | 62 | 1.6 | 0.33 | 0.35 | 0.32 | 0.63 | 0.60 | 0.45 | 100.0 | 10.0 | 7.0 |
sec | 2001_03 | dssp | 1hn5:D | 58.0 | 60 | 63 | 76 | 56 | 49 | 52 | 57.9 | 55 | 86 | 52 | 4.8 | 0.14 | 0.15 | 0.15 | 0.26 | 0.60 | 0.20 | 100.0 | 2.0 | 4.0 |
sec | 2001_03 | dssp | 1hn5:E | 58.3 | 72 | 54 | 76 | 52 | 43 | 67 | 49.1 | 51 | 88 | 40 | 3.0 | 0.16 | 0.17 | 0.16 | 0.32 | 0.57 | 0.24 | 100.0 | 12.0 | 4.0 |
sec | 2001_03 | dssp | 1hn5:F | 67.4 | 78 | 67 | 65 | 70 | 54 | 65 | 71.4 | 73 | 81 | 64 | 3.0 | 0.22 | 0.22 | 0.23 | 0.47 | 0.62 | 0.37 | 100.0 | 7.0 | 0.00 |
sec | 2001_03 | dssp | 1hux:A | 71.8 | 77 | 86 | 66 | 62 | 68 | 63 | 68.3 | 84 | 78 | 48 | 3.8 | 0.32 | 0.33 | 0.33 | 0.69 | 0.53 | 0.46 | 100.0 | 4.0 | 1.0 |
sec | 2001_03 | dssp | 1hx1:B | 82.1 | 93 | 85 | 0 | 0 | 41 | 62 | 69.1 | 73 | 100 | 47 | 0.0 | 0.15 | 0.13 | 0.17 | 0.40 | 1.0 | 0.40 | 100.0 | 7.0 | 0.00 |
sec | 2001_03 | dssp | 1i17:A | 70.1 | 84 | 73 | 33 | 22 | 58 | 75 | 68.3 | 87 | 21 | 55 | 2.8 | 0.23 | 0.23 | 0.23 | 0.55 | 0.21 | 0.45 | 100.0 | 7.0 | 2.0 |
sec | 2001_03 | dssp | 1i1r:B | 82.0 | 94 | 81 | 0 | 0 | 62 | 84 | 87.5 | 93 | 0 | 80 | 0.5 | 0.30 | 0.28 | 0.34 | 0.61 | 1.0 | 0.61 | 100.0 | 10.0 | 1.0 |
sec | 2001_03 | dssp | 1i2j:A | 46.5 | 47 | 47 | 100 | 1 | 45 | 92 | 35.1 | 37 | 13 | 34 | 16.0 | 0.11 | 0.15 | 0.09 | 0.19 | 0.08 | 0.40 | 0.0 | 0.00 | 33.0 |
sec | 2001_03 | dssp | 1i7o:A | 68.9 | 74 | 55 | 50 | 76 | 78 | 71 | 57.7 | 54 | 53 | 61 | 4.2 | 0.23 | 0.23 | 0.23 | 0.56 | 0.49 | 0.46 | 100.0 | 5.0 | 11.0 |
sec | 2001_03 | dssp | 1i9a:A | 60.7 | 60 | 60 | 43 | 66 | 75 | 58 | 52.8 | 66 | 42 | 52 | 7.3 | 0.14 | 0.14 | 0.15 | 0.46 | 0.36 | 0.37 | 100.0 | 0.00 | 11.0 |
sec | 2001_03 | dssp | THIS_month:psum | 70.9 | 70 | 70 | 48 | 41 | 66 | 69 | 65.0 | 70.1 | 59.0 | 58.9 | 4.0 | 0.25 | 0.25 | 0.25 | 0.57 | 0.56 | 0.45 | 85.7 | 6.9 | 5.2 |
sec | 2001_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 | 2001_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 | 2001_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) ) |