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_01 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_01 | 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_01 | 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_01 | 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_01 | dssp | THIS_month:psum | 67.9 | 61 | 65 | 39 | 37 | 65 | 65 | 62.4 | 72.0 | 63.8 | 59.2 | 5.5 | 0.21 | 0.21 | 0.20 | 0.55 | 0.53 | 0.42 | 77.7 | 8.3 | 6.4 |
sec | 2002_01 | dssp | 1ear:A | 62.0 | 90 | 53 | 54 | 66 | 53 | 66 | 61.4 | 88 | 58 | 51 | 9.1 | 0.22 | 0.23 | 0.22 | 0.58 | 0.39 | 0.37 | 0.0 | 14.0 | 7.0 |
sec | 2002_01 | dssp | 1ez4:A | 63.0 | 55 | 86 | 81 | 65 | 60 | 45 | 63.4 | 73 | 74 | 41 | 1.3 | 0.29 | 0.30 | 0.29 | 0.52 | 0.63 | 0.25 | 0.0 | 16.0 | 5.0 |
sec | 2002_01 | dssp | 1ez4:B | 63.0 | 55 | 86 | 81 | 65 | 60 | 45 | 63.4 | 73 | 74 | 41 | 1.3 | 0.29 | 0.30 | 0.29 | 0.52 | 0.63 | 0.25 | 0.0 | 16.0 | 5.0 |
sec | 2002_01 | dssp | 1hj0:A | 53.7 | 40 | 100 | 0 | 0 | 100 | 32 | 54.3 | 56 | 100 | 47 | 0.0 | 0.17 | 0.18 | 0.16 | 0.36 | 1.0 | 0.36 | 100.0 | 46.0 | 0.00 |
sec | 2002_01 | dssp | 1hty:A | 61.9 | 68 | 54 | 41 | 58 | 72 | 67 | 56.6 | 63 | 49 | 57 | 8.9 | 0.14 | 0.15 | 0.15 | 0.47 | 0.32 | 0.41 | 100.0 | 5.0 | 8.0 |
sec | 2002_01 | dssp | 1hzm:A | 57.1 | 61 | 46 | 81 | 28 | 52 | 81 | 56.6 | 50 | 51 | 59 | 4.5 | 0.12 | 0.14 | 0.11 | 0.30 | 0.41 | 0.29 | 100.0 | 9.0 | 13.0 |
sec | 2002_01 | dssp | 1ijh:A | 65.7 | 58 | 65 | 64 | 59 | 70 | 69 | 63.5 | 66 | 68 | 59 | 5.6 | 0.18 | 0.19 | 0.19 | 0.47 | 0.49 | 0.42 | 100.0 | 3.0 | 2.0 |
sec | 2002_01 | dssp | 1ijl:A | 48.8 | 18 | 91 | 55 | 13 | 78 | 60 | 49.1 | 25 | 52 | 72 | 17.8 | 0.10 | 0.10 | 0.10 | 0.29 | 0.14 | 0.35 | 100.0 | 37.0 | 23.0 |
sec | 2002_01 | dssp | 1jad:A | 88.4 | 92 | 94 | 0 | 0 | 62 | 73 | 57.6 | 55 | 100 | 85 | 2.8 | 0.31 | 0.35 | 0.27 | 0.58 | 1.0 | 0.62 | 100.0 | 1.0 | 3.0 |
sec | 2002_01 | dssp | 1jgk:A | 68.2 | 0 | 0 | 60 | 65 | 73 | 83 | 75.9 | 100 | 64 | 83 | 6.0 | 0.15 | 0.18 | 0.13 | 1.0 | 0.41 | 0.47 | 100.0 | 10.0 | 3.0 |
sec | 2002_01 | dssp | 1jgs:A | 64.5 | 76 | 77 | 63 | 28 | 39 | 57 | 73.9 | 91 | 72 | 42 | 8.6 | 0.12 | 0.13 | 0.12 | 0.40 | 0.34 | 0.30 | 100.0 | 0.00 | 10.0 |
sec | 2002_01 | dssp | 1jh1:A | 64.6 | 73 | 54 | 36 | 33 | 68 | 81 | 58.8 | 84 | 37 | 55 | 6.9 | 0.15 | 0.16 | 0.15 | 0.49 | 0.21 | 0.43 | 100.0 | 8.0 | 1.0 |
sec | 2002_01 | dssp | 1jke:A | 69.0 | 85 | 61 | 68 | 73 | 58 | 70 | 53.2 | 88 | 42 | 52 | 8.2 | 0.26 | 0.27 | 0.27 | 0.62 | 0.51 | 0.47 | 0.0 | 8.0 | 2.0 |
sec | 2002_01 | dssp | 1joc:A | 62.6 | 71 | 83 | 25 | 21 | 59 | 50 | 40.2 | 39 | 23 | 46 | 3.2 | 0.16 | 0.17 | 0.16 | 0.52 | 0.14 | 0.27 | 100.0 | 8.0 | 1.0 |
sec | 2002_01 | dssp | 1jr8:A | 78.1 | 86 | 82 | 0 | 0 | 60 | 76 | 82.4 | 90 | 100 | 63 | 3.8 | 0.23 | 0.26 | 0.22 | 0.48 | 1.0 | 0.56 | 100.0 | 2.0 | 3.0 |
sec | 2002_01 | dssp | 1jr8:B | 79.0 | 83 | 86 | 0 | 0 | 67 | 75 | 72.8 | 73 | 100 | 72 | 4.7 | 0.26 | 0.30 | 0.24 | 0.50 | 1.0 | 0.60 | 100.0 | 1.0 | 4.0 |
sec | 2002_01 | dssp | 1jra:A | 78.3 | 87 | 82 | 0 | 0 | 60 | 84 | 83.1 | 90 | 100 | 67 | 4.7 | 0.26 | 0.28 | 0.24 | 0.51 | 1.0 | 0.60 | 0.0 | 3.0 | 5.0 |
sec | 2002_01 | dssp | 1jra:C | 79.0 | 88 | 82 | 0 | 0 | 60 | 80 | 82.8 | 90 | 100 | 67 | 2.8 | 0.24 | 0.26 | 0.23 | 0.53 | 1.0 | 0.57 | 100.0 | 4.0 | 3.0 |
sec | 2002_01 | dssp | 1jra:D | 74.8 | 81 | 82 | 0 | 0 | 61 | 67 | 80.7 | 89 | 100 | 63 | 2.9 | 0.16 | 0.18 | 0.15 | 0.45 | 1.0 | 0.48 | 100.0 | 0.00 | 3.0 |
sec | 2002_01 | dssp | 1jy8:A | 60.6 | 73 | 73 | 41 | 62 | 64 | 49 | 51.2 | 76 | 30 | 52 | 5.8 | 0.21 | 0.21 | 0.22 | 0.58 | 0.34 | 0.30 | 0.0 | 0.00 | 10.0 |
sec | 2002_01 | dssp | 1k04:A | 89.4 | 93 | 92 | 0 | 0 | 74 | 76 | 77.1 | 77 | 100 | 77 | 0.0 | 0.39 | 0.39 | 0.40 | 0.68 | 1.0 | 0.68 | 100.0 | 0.00 | 0.00 |
sec | 2002_01 | dssp | 1k2f:A | 49.5 | 81 | 33 | 23 | 66 | 60 | 63 | 47.9 | 74 | 31 | 50 | 21.0 | 0.11 | 0.12 | 0.12 | 0.33 | 0.21 | 0.37 | 100.0 | 28.0 | 26.0 |
sec | 2002_01 | dssp | 1k7c:A | 65.2 | 55 | 91 | 86 | 36 | 66 | 76 | 57.9 | 63 | 83 | 48 | 10.7 | 0.26 | 0.27 | 0.26 | 0.59 | 0.44 | 0.51 | 100.0 | 15.0 | 21.0 |
sec | 2002_01 | dssp | 1k8t:A | 66.5 | 73 | 76 | 47 | 42 | 65 | 66 | 61.3 | 75 | 50 | 52 | 5.4 | 0.19 | 0.20 | 0.19 | 0.56 | 0.34 | 0.42 | 100.0 | 1.0 | 1.0 |
sec | 2002_01 | dssp | 1k9q:A | 85.0 | 0 | 0 | 61 | 88 | 96 | 83 | 80.0 | 100 | 69 | 85 | 0.0 | 0.36 | 0.33 | 0.39 | 1.0 | 0.64 | 0.64 | 100.0 | 0.00 | 10.0 |
sec | 2002_01 | dssp | 1k9r:A | 85.0 | 0 | 0 | 60 | 100 | 100 | 80 | 76.0 | 100 | 66 | 81 | 0.0 | 0.47 | 0.42 | 0.53 | 1.0 | 0.69 | 0.69 | 100.0 | 0.00 | 15.0 |
sec | 2002_01 | dssp | 1kb0:A | 65.6 | 42 | 41 | 64 | 66 | 71 | 70 | 60.0 | 45 | 64 | 59 | 3.4 | 0.14 | 0.15 | 0.15 | 0.34 | 0.45 | 0.38 | 100.0 | 0.00 | 0.00 |
sec | 2002_01 | dssp | 1kbe:A | 46.9 | 0 | 0 | 36 | 30 | 50 | 76 | 52.0 | 100 | 36 | 56 | 2.0 | 0.02 | 0.04 | 0.02 | 1.0 | 0.11 | -0.03 | 100.0 | 22.0 | 4.0 |
sec | 2002_01 | dssp | 1khv:B | 64.0 | 75 | 72 | 38 | 41 | 62 | 63 | 57.5 | 65 | 45 | 54 | 6.8 | 0.17 | 0.17 | 0.17 | 0.53 | 0.28 | 0.38 | 100.0 | 2.0 | 1.0 |
sec | 2002_01 | dssp | 1kkc:A | 69.5 | 80 | 80 | 32 | 47 | 63 | 55 | 46.8 | 41 | 44 | 63 | 4.5 | 0.22 | 0.22 | 0.23 | 0.54 | 0.31 | 0.40 | 100.0 | 0.00 | 3.0 |
sec | 2002_01 | dssp | 1kkc:B | 69.3 | 81 | 80 | 32 | 47 | 61 | 55 | 53.1 | 51 | 44 | 59 | 4.0 | 0.22 | 0.21 | 0.23 | 0.55 | 0.31 | 0.38 | 100.0 | 0.00 | 4.0 |
sec | 2002_01 | dssp | 1kkc:X | 70.0 | 82 | 81 | 32 | 47 | 62 | 56 | 53.4 | 51 | 44 | 60 | 4.0 | 0.22 | 0.22 | 0.23 | 0.57 | 0.31 | 0.40 | 100.0 | 1.0 | 3.0 |
sec | 2002_01 | dssp | 1kni:A | 73.5 | 73 | 86 | 93 | 63 | 66 | 54 | 66.8 | 67 | 93 | 55 | 3.7 | 0.30 | 0.32 | 0.28 | 0.50 | 0.74 | 0.44 | 100.0 | 9.0 | 4.0 |
sec | 2002_01 | dssp | 1knz:A | 63.9 | 59 | 92 | 0 | 0 | 80 | 45 | 70.2 | 72 | 100 | 62 | 13.8 | 0.18 | 0.25 | 0.12 | 0.32 | 1.0 | 0.48 | 0.0 | 28.0 | 13.0 |
sec | 2002_01 | dssp | 1kov:A | 72.4 | 0 | 0 | 56 | 44 | 77 | 84 | 55.6 | 100 | 37 | 60 | 0.0 | 0.08 | 0.09 | 0.08 | 1.0 | 0.31 | 0.31 | 100.0 | 0.00 | 6.0 |
sec | 2002_01 | dssp | 1kpl:B | 67.6 | 76 | 82 | 0 | 0 | 39 | 56 | 51.0 | 55 | 0 | 39 | 11.7 | 0.09 | 0.11 | 0.08 | 0.23 | -0.04 | 0.35 | 0.0 | 5.0 | 11.0 |
sec | 2002_01 | dssp | THIS_month:psum | 67.9 | 61 | 65 | 39 | 37 | 65 | 65 | 62.4 | 72.0 | 63.8 | 59.2 | 5.5 | 0.21 | 0.21 | 0.20 | 0.55 | 0.53 | 0.42 | 77.7 | 8.3 | 6.4 |
sec | 2002_01 | 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_01 | 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_01 | 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) ) |