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_05 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_05 | 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_05 | 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_05 | 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_05 | dssp | THIS_month:psum | 66.9 | 55 | 62 | 41 | 42 | 67 | 67 | 60.6 | 55.4 | 67.1 | 60.2 | 5.5 | 0.21 | 0.20 | 0.23 | 0.45 | 0.59 | 0.40 | 76.3 | 10.7 | 7.8 |
sec | 2002_05 | dssp | 1cix:A | 75.0 | 0 | 0 | 36 | 50 | 87 | 80 | 56.3 | 100 | 34 | 63 | 0.0 | 0.06 | 0.06 | 0.07 | 1.0 | 0.27 | 0.27 | 100.0 | 0.00 | 6.0 |
sec | 2002_05 | dssp | 1go4:G | 75.0 | 98 | 74 | 0 | 0 | 23 | 83 | 46.3 | 56 | 0 | 28 | 8.0 | 0.16 | 0.08 | 0.26 | 0.30 | 1.0 | 0.38 | 0.0 | 23.0 | 8.0 |
sec | 2002_05 | dssp | 1hxv:A | 78.8 | 66 | 100 | 74 | 76 | 84 | 77 | 74.8 | 66 | 88 | 68 | 0.0 | 0.40 | 0.39 | 0.42 | 0.80 | 0.61 | 0.57 | 100.0 | 3.0 | 1.0 |
sec | 2002_05 | dssp | 1i36:A | 73.2 | 80 | 92 | 57 | 50 | 67 | 55 | 77.3 | 86 | 60 | 66 | 2.4 | 0.33 | 0.34 | 0.32 | 0.70 | 0.45 | 0.43 | 100.0 | 7.0 | 1.0 |
sec | 2002_05 | dssp | 1iko:P | 70.2 | 0 | 0 | 83 | 61 | 75 | 79 | 61.1 | 0 | 81 | 60 | 3.5 | 0.21 | 0.19 | 0.23 | -0.04 | 0.56 | 0.46 | 100.0 | 7.0 | 11.0 |
sec | 2002_05 | dssp | 1ir6:A | 73.8 | 83 | 77 | 55 | 62 | 67 | 71 | 73.8 | 82 | 56 | 68 | 3.3 | 0.27 | 0.27 | 0.28 | 0.59 | 0.53 | 0.51 | 100.0 | 3.0 | 1.0 |
sec | 2002_05 | dssp | 1jjv:A | 84.5 | 96 | 80 | 100 | 81 | 65 | 93 | 90.2 | 97 | 100 | 78 | 0.0 | 0.59 | 0.59 | 0.59 | 0.77 | 0.88 | 0.68 | 100.0 | 8.0 | 3.0 |
sec | 2002_05 | dssp | 1jni:A | 54.8 | 0 | 0 | 25 | 5 | 75 | 75 | 50.7 | 0 | 33 | 68 | 9.6 | 0.01 | 0.02 | 0.02 | 1.0 | -0.02 | 0.13 | 100.0 | 22.0 | 22.0 |
sec | 2002_05 | dssp | 1jsx:A | 91.4 | 100 | 89 | 0 | 0 | 66 | 100 | 97.1 | 100 | 100 | 88 | 0.0 | 0.57 | 0.52 | 0.64 | 0.77 | 1.0 | 0.77 | 100.0 | 8.0 | 0.00 |
sec | 2002_05 | dssp | 1juh:B | 73.4 | 30 | 100 | 76 | 70 | 76 | 74 | 70.7 | 40 | 72 | 73 | 1.9 | 0.23 | 0.22 | 0.25 | 0.53 | 0.51 | 0.50 | 0.0 | 4.0 | 3.0 |
sec | 2002_05 | dssp | 1k3r:B | 68.2 | 63 | 58 | 67 | 59 | 71 | 80 | 71.9 | 59 | 68 | 80 | 9.0 | 0.22 | 0.22 | 0.22 | 0.44 | 0.51 | 0.54 | 100.0 | 2.0 | 3.0 |
sec | 2002_05 | dssp | 1k45:A | 57.7 | 0 | 0 | 70 | 55 | 49 | 61 | 44.4 | 0 | 48 | 41 | 1.7 | 0.02 | 0.03 | 0.03 | 1.0 | 0.20 | 0.19 | 100.0 | 3.0 | 13.0 |
sec | 2002_05 | dssp | 1kjy:B | 57.1 | 58 | 55 | 0 | 0 | 55 | 58 | 50.4 | 58 | 100 | 42 | 0.0 | 0.01 | 0.01 | 0.01 | 0.14 | 1.0 | 0.14 | 100.0 | 2.0 | 0.00 |
sec | 2002_05 | dssp | 1kpp:A | 48.6 | 18 | 50 | 43 | 21 | 65 | 71 | 46.7 | 18 | 37 | 61 | 19.4 | 0.11 | 0.11 | 0.11 | 0.17 | 0.01 | 0.36 | 100.0 | 16.0 | 20.0 |
sec | 2002_05 | dssp | 1kr7:A | 84.5 | 87 | 90 | 0 | 0 | 76 | 69 | 84.7 | 89 | 100 | 71 | 0.0 | 0.31 | 0.32 | 0.31 | 0.62 | 1.0 | 0.62 | 100.0 | 2.0 | 0.00 |
sec | 2002_05 | dssp | 1ksh:B | 50.0 | 56 | 24 | 36 | 82 | 74 | 51 | 51.7 | 81 | 40 | 63 | 22.7 | 0.12 | 0.13 | 0.11 | 0.19 | 0.29 | 0.42 | 0.0 | 19.0 | 31.0 |
sec | 2002_05 | dssp | 1ktg:A | 55.5 | 92 | 44 | 13 | 100 | 83 | 67 | 44.8 | 66 | 20 | 61 | 29.1 | 0.27 | 0.24 | 0.31 | 0.41 | 0.28 | 0.64 | 100.0 | 31.0 | 37.0 |
sec | 2002_05 | dssp | 1kuu:A | 70.8 | 68 | 59 | 60 | 77 | 81 | 72 | 72.4 | 78 | 63 | 78 | 8.9 | 0.26 | 0.26 | 0.26 | 0.53 | 0.51 | 0.59 | 100.0 | 2.0 | 8.0 |
sec | 2002_05 | dssp | 1kv4:A | 92.9 | 93 | 96 | 0 | 0 | 91 | 84 | 73.9 | 68 | 100 | 100 | 0.0 | 0.59 | 0.60 | 0.58 | 0.83 | 1.0 | 0.83 | 100.0 | 2.0 | 0.00 |
sec | 2002_05 | dssp | 1kyq:B | 64.1 | 72 | 62 | 52 | 80 | 60 | 61 | 66.2 | 77 | 60 | 56 | 5.8 | 0.19 | 0.19 | 0.20 | 0.38 | 0.59 | 0.36 | 100.0 | 6.0 | 6.0 |
sec | 2002_05 | dssp | 1l1d:B | 60.5 | 17 | 87 | 50 | 60 | 91 | 58 | 48.5 | 17 | 55 | 61 | 5.4 | 0.15 | 0.13 | 0.19 | 0.33 | 0.40 | 0.39 | 100.0 | 21.0 | 4.0 |
sec | 2002_05 | dssp | 1l1s:A | 44.1 | 13 | 38 | 85 | 41 | 59 | 51 | 44.2 | 18 | 79 | 56 | 27.9 | 0.16 | 0.16 | 0.17 | -0.07 | 0.39 | 0.35 | 0.0 | 30.0 | 26.0 |
sec | 2002_05 | dssp | 1ldj:A | 81.8 | 100 | 80 | 0 | 0 | 28 | 100 | 64.4 | 74 | 100 | 35 | 0.0 | 0.30 | 0.19 | 0.41 | 0.47 | 1.0 | 0.47 | 100.0 | 18.0 | 0.00 |
sec | 2002_05 | dssp | 1ldj:B | 68.2 | 63 | 53 | 30 | 50 | 82 | 74 | 50.2 | 49 | 26 | 56 | 2.2 | 0.15 | 0.15 | 0.16 | 0.52 | 0.25 | 0.32 | 100.0 | 2.0 | 9.0 |
sec | 2002_05 | dssp | 1ldv:A | 57.2 | 10 | 33 | 14 | 27 | 86 | 63 | 21.3 | 15 | 4 | 28 | 4.9 | 0.06 | 0.05 | 0.08 | 0.11 | 0.01 | 0.15 | 100.0 | 9.0 | 12.0 |
sec | 2002_05 | dssp | 1lgj:A | 62.5 | 81 | 69 | 0 | 0 | 29 | 50 | 50.6 | 71 | 100 | 21 | 1.1 | 0.03 | 0.04 | 0.04 | 0.20 | 1.0 | 0.14 | 100.0 | 10.0 | 4.0 |
sec | 2002_05 | dssp | 1lgo:A | 57.4 | 64 | 78 | 0 | 0 | 43 | 46 | 55.2 | 60 | 100 | 42 | 6.4 | 0.05 | 0.07 | 0.04 | 0.29 | 1.0 | 0.18 | 0.0 | 11.0 | 14.0 |
sec | 2002_05 | dssp | 1lgz:A | 45.1 | 23 | 55 | 0 | 0 | 74 | 41 | 48.0 | 35 | 100 | 65 | 0.0 | 0.00 | 0.00 | 0.00 | -0.02 | 1.0 | -0.02 | 0.0 | 32.0 | 0.00 |
sec | 2002_05 | dssp | 1lh8:A | 56.2 | 56 | 82 | 0 | 0 | 56 | 26 | 40.1 | 39 | 100 | 43 | 0.0 | 0.00 | 0.01 | 0.01 | 0.10 | 1.0 | 0.10 | 100.0 | 24.0 | 0.00 |
sec | 2002_05 | dssp | 1li1:A | 68.0 | 4 | 16 | 62 | 82 | 87 | 62 | 55.4 | 3 | 56 | 64 | 2.1 | 0.19 | 0.17 | 0.21 | 0.03 | 0.54 | 0.44 | 100.0 | 7.0 | 10.0 |
sec | 2002_05 | dssp | 1li5:A | 84.8 | 89 | 96 | 62 | 83 | 91 | 75 | 79.5 | 92 | 65 | 73 | 0.6 | 0.56 | 0.56 | 0.58 | 0.88 | 0.66 | 0.71 | 100.0 | 3.0 | 5.0 |
sec | 2002_05 | dssp | 1lja:A | 68.0 | 82 | 74 | 0 | 0 | 33 | 46 | 59.8 | 69 | 100 | 34 | 1.3 | 0.03 | 0.04 | 0.04 | 0.17 | 1.0 | 0.19 | 100.0 | 7.0 | 1.0 |
sec | 2002_05 | dssp | 1lk8:A | 51.0 | 45 | 43 | 51 | 35 | 54 | 66 | 47.6 | 47 | 47 | 47 | 11.7 | 0.05 | 0.06 | 0.05 | 0.18 | 0.27 | 0.26 | 0.0 | 1.0 | 8.0 |
sec | 2002_05 | dssp | 1ll3:A | 66.5 | 65 | 83 | 59 | 50 | 71 | 63 | 66.5 | 69 | 62 | 64 | 6.0 | 0.23 | 0.23 | 0.23 | 0.59 | 0.41 | 0.43 | 0.0 | 9.0 | 3.0 |
sec | 2002_05 | dssp | 1ln4:A | 88.8 | 92 | 88 | 80 | 84 | 89 | 91 | 94.8 | 100 | 82 | 96 | 4.0 | 0.64 | 0.65 | 0.65 | 0.83 | 0.77 | 0.84 | 100.0 | 2.0 | 1.0 |
sec | 2002_05 | dssp | 1lpl:A | 68.4 | 27 | 100 | 87 | 57 | 66 | 77 | 72.3 | 36 | 78 | 76 | 2.1 | 0.24 | 0.23 | 0.26 | 0.49 | 0.52 | 0.42 | 0.0 | 8.0 | 16.0 |
sec | 2002_05 | dssp | 1lr0:A | 50.0 | 24 | 80 | 78 | 58 | 84 | 37 | 50.6 | 30 | 71 | 73 | 9.5 | 0.18 | 0.19 | 0.19 | 0.22 | 0.58 | 0.31 | 100.0 | 38.0 | 6.0 |
sec | 2002_05 | dssp | 1lu7:A | 65.1 | 83 | 68 | 66 | 40 | 49 | 71 | 51.6 | 61 | 65 | 42 | 0.7 | 0.23 | 0.24 | 0.23 | 0.55 | 0.45 | 0.32 | 100.0 | 8.0 | 6.0 |
sec | 2002_05 | dssp | THIS_month:psum | 66.9 | 55 | 62 | 41 | 42 | 67 | 67 | 60.6 | 55.4 | 67.1 | 60.2 | 5.5 | 0.21 | 0.20 | 0.23 | 0.45 | 0.59 | 0.40 | 76.3 | 10.7 | 7.8 |
sec | 2002_05 | 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_05 | 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_05 | 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) ) |