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_04 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_04 | 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_04 | 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_04 | 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_04 | dssp | THIS_month:psum | 70.8 | 64 | 61 | 40 | 49 | 69 | 70 | 64.3 | 63.5 | 70.2 | 59.5 | 3.6 | 0.27 | 0.27 | 0.28 | 0.54 | 0.63 | 0.47 | 72.7 | 9.9 | 6.6 |
sec | 2002_04 | dssp | 1ich:A | 75.9 | 82 | 84 | 0 | 0 | 56 | 68 | 79.9 | 85 | 100 | 63 | 5.7 | 0.19 | 0.21 | 0.17 | 0.38 | 1.0 | 0.50 | 0.0 | 1.0 | 5.0 |
sec | 2002_04 | dssp | 1icz:A | 41.8 | 72 | 23 | 13 | 10 | 36 | 82 | 28.0 | 38 | 5 | 27 | 4.8 | 0.01 | 0.02 | 0.01 | 0.13 | 0.04 | 0.12 | 100.0 | 40.0 | 2.0 |
sec | 2002_04 | dssp | 1jki:A | 71.2 | 69 | 77 | 54 | 80 | 83 | 64 | 62.5 | 67 | 56 | 62 | 4.1 | 0.28 | 0.28 | 0.30 | 0.60 | 0.57 | 0.52 | 0.0 | 3.0 | 8.0 |
sec | 2002_04 | dssp | 1jww:A | 86.2 | 95 | 95 | 80 | 77 | 83 | 85 | 90.7 | 100 | 89 | 85 | 0.0 | 0.61 | 0.62 | 0.61 | 0.93 | 0.71 | 0.72 | 100.0 | 0.00 | 1.0 |
sec | 2002_04 | dssp | 1jyh:A | 61.3 | 58 | 44 | 50 | 77 | 75 | 63 | 56.9 | 68 | 52 | 55 | 13.5 | 0.16 | 0.17 | 0.17 | 0.33 | 0.45 | 0.48 | 100.0 | 7.0 | 14.0 |
sec | 2002_04 | dssp | 1k1v:A | 87.8 | 89 | 92 | 0 | 0 | 84 | 78 | 82.5 | 84 | 100 | 78 | 0.0 | 0.43 | 0.44 | 0.42 | 0.72 | 1.0 | 0.72 | 100.0 | 2.0 | 0.00 |
sec | 2002_04 | dssp | 1k2e:A | 66.4 | 75 | 84 | 59 | 70 | 66 | 52 | 58.4 | 58 | 63 | 51 | 1.9 | 0.29 | 0.29 | 0.29 | 0.72 | 0.46 | 0.34 | 100.0 | 3.0 | 5.0 |
sec | 2002_04 | dssp | 1k3b:A | 74.8 | 0 | 0 | 78 | 83 | 76 | 79 | 69.4 | 0 | 78 | 64 | 6.7 | 0.32 | 0.34 | 0.30 | -0.05 | 0.59 | 0.61 | 0.0 | 5.0 | 3.0 |
sec | 2002_04 | dssp | 1k3k:A | 78.1 | 91 | 77 | 0 | 0 | 56 | 79 | 74.7 | 71 | 100 | 81 | 0.0 | 0.22 | 0.21 | 0.23 | 0.52 | 1.0 | 0.52 | 100.0 | 10.0 | 0.00 |
sec | 2002_04 | dssp | 1k81:A | 61.1 | 0 | 0 | 31 | 85 | 94 | 61 | 45.6 | 100 | 36 | 51 | 8.3 | 0.17 | 0.19 | 0.17 | 1.0 | 0.32 | 0.46 | 100.0 | 8.0 | 33.0 |
sec | 2002_04 | dssp | 1k8b:A | 71.2 | 95 | 74 | 38 | 100 | 76 | 55 | 67.1 | 91 | 44 | 59 | 7.6 | 0.38 | 0.36 | 0.40 | 0.71 | 0.54 | 0.51 | 100.0 | 11.0 | 21.0 |
sec | 2002_04 | dssp | 1ksk:A | 77.3 | 76 | 81 | 75 | 72 | 78 | 78 | 83.2 | 84 | 83 | 82 | 1.2 | 0.37 | 0.38 | 0.38 | 0.73 | 0.63 | 0.57 | 100.0 | 1.0 | 1.0 |
sec | 2002_04 | dssp | 1ku3:A | 73.8 | 91 | 71 | 0 | 0 | 48 | 80 | 76.7 | 92 | 100 | 53 | 0.0 | 0.17 | 0.15 | 0.19 | 0.45 | 1.0 | 0.45 | 100.0 | 16.0 | 0.00 |
sec | 2002_04 | dssp | 1kv8:B | 84.7 | 90 | 85 | 83 | 78 | 76 | 88 | 90.0 | 94 | 86 | 85 | 4.6 | 0.49 | 0.50 | 0.50 | 0.75 | 0.75 | 0.74 | 0.0 | 2.0 | 1.0 |
sec | 2002_04 | dssp | 1kxl:A | 63.6 | 91 | 48 | 62 | 52 | 51 | 94 | 44.8 | 50 | 49 | 42 | 7.4 | 0.25 | 0.26 | 0.24 | 0.51 | 0.46 | 0.51 | 0.0 | 21.0 | 3.0 |
sec | 2002_04 | dssp | 1ky9:B | 52.9 | 50 | 45 | 38 | 100 | 70 | 43 | 56.9 | 72 | 52 | 55 | 0.0 | 0.27 | 0.25 | 0.29 | 0.34 | 0.51 | 0.12 | 100.0 | 1.0 | 25.0 |
sec | 2002_04 | dssp | 1l0o:A | 68.1 | 50 | 96 | 85 | 52 | 75 | 68 | 61.9 | 57 | 81 | 55 | 9.9 | 0.30 | 0.30 | 0.30 | 0.59 | 0.53 | 0.54 | 0.0 | 18.0 | 14.0 |
sec | 2002_04 | dssp | 1l0o:C | 66.7 | 64 | 100 | 0 | 0 | 78 | 40 | 62.1 | 71 | 0 | 45 | 0.0 | 0.34 | 0.40 | 0.29 | 0.56 | -0.03 | 0.35 | 100.0 | 26.0 | 3.0 |
sec | 2002_04 | dssp | 1l3y:A | 80.5 | 0 | 0 | 75 | 75 | 93 | 81 | 67.6 | 0 | 100 | 67 | 0.0 | 0.33 | 0.26 | 0.42 | 1.0 | 0.68 | 0.49 | 100.0 | 9.0 | 0.00 |
sec | 2002_04 | dssp | 1l7j:A | 72.8 | 42 | 42 | 71 | 80 | 79 | 71 | 65.0 | 38 | 72 | 62 | 2.0 | 0.24 | 0.25 | 0.25 | 0.37 | 0.58 | 0.50 | 100.0 | 0.00 | 5.0 |
sec | 2002_04 | dssp | 1l8c:B | 72.5 | 47 | 69 | 0 | 0 | 87 | 75 | 66.2 | 48 | 100 | 76 | 1.9 | 0.15 | 0.15 | 0.15 | 0.38 | 1.0 | 0.43 | 100.0 | 11.0 | 1.0 |
sec | 2002_04 | dssp | 1l8m:A | 69.3 | 96 | 71 | 0 | 0 | 11 | 61 | 24.7 | 30 | 100 | 12 | 0.0 | 0.07 | 0.05 | 0.10 | 0.23 | 1.0 | 0.15 | 100.0 | 24.0 | 1.0 |
sec | 2002_04 | dssp | THIS_month:psum | 70.8 | 64 | 61 | 40 | 49 | 69 | 70 | 64.3 | 63.5 | 70.2 | 59.5 | 3.6 | 0.27 | 0.27 | 0.28 | 0.54 | 0.63 | 0.47 | 72.7 | 9.9 | 6.6 |
sec | 2002_04 | 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_04 | 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_04 | 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) ) |