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_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 | 2000_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 | 2000_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 | 2000_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 | 2000_05 | dssp | THIS_month:psum | 72.6 | 81 | 68 | 41 | 53 | 68 | 75 | 73.1 | 79 | 67.2 | 68.1 | 4.3 | 0.31 | 0.32 | 0.31 | 0.54 | 0.62 | 0.54 | 57.1 | 9.8 | 4.9 |
sec | 2000_05 | dssp | 1d9e:A | 75.6 | 90 | 76 | 62 | 81 | 67 | 71 | 77.1 | 87 | 71 | 69 | 1.8 | 0.37 | 0.37 | 0.38 | 0.69 | 0.64 | 0.51 | 0.0 | 7.0 | 4.0 |
sec | 2000_05 | dssp | 1dj0:A | 81.8 | 85 | 74 | 79 | 89 | 81 | 82 | 90.3 | 89 | 91 | 90 | 0.7 | 0.48 | 0.48 | 0.48 | 0.72 | 0.78 | 0.65 | 100.0 | 3.0 | 3.0 |
sec | 2000_05 | dssp | 1dlj:A | 79.6 | 82 | 85 | 77 | 58 | 77 | 82 | 74.2 | 79 | 77 | 67 | 3.9 | 0.39 | 0.40 | 0.38 | 0.71 | 0.61 | 0.66 | 100.0 | 1.0 | 4.0 |
sec | 2000_05 | dssp | 1dny:A | 80.3 | 92 | 81 | 0 | 0 | 64 | 88 | 73.7 | 100 | 100 | 52 | 0.0 | 0.35 | 0.38 | 0.33 | 0.68 | 1.0 | 0.60 | 100.0 | 7.0 | 3.0 |
sec | 2000_05 | dssp | 1du2:A | 56.6 | 100 | 45 | 0 | 0 | 32 | 100 | 49.5 | 76 | 100 | 37 | 0.0 | 0.18 | 0.17 | 0.21 | 0.38 | 1.0 | 0.38 | 0.0 | 43.0 | 0.00 |
sec | 2000_05 | dssp | 1e0b:A | 54.1 | 37 | 31 | 38 | 88 | 79 | 57 | 66.4 | 56 | 47 | 89 | 14.7 | 0.19 | 0.18 | 0.21 | 0.08 | 0.47 | 0.40 | 100.0 | 4.0 | 19.0 |
sec | 2000_05 | dssp | 1edu:A | 85.2 | 85 | 93 | 50 | 100 | 85 | 68 | 89.1 | 93 | 50 | 78 | 0.0 | 0.39 | 0.40 | 0.39 | 0.67 | 0.70 | 0.65 | 100.0 | 6.0 | 0.00 |
sec | 2000_05 | dssp | 1ef1:A | 81.0 | 91 | 82 | 68 | 82 | 78 | 78 | 84.5 | 92 | 82 | 78 | 3.4 | 0.45 | 0.45 | 0.46 | 0.78 | 0.67 | 0.66 | 100.0 | 4.0 | 4.0 |
sec | 2000_05 | dssp | 1ef1:C | 75.6 | 82 | 76 | 0 | 0 | 68 | 78 | 68.0 | 66 | 0 | 71 | 3.3 | 0.23 | 0.23 | 0.23 | 0.49 | -0.01 | 0.56 | 100.0 | 4.0 | 1.0 |
sec | 2000_05 | dssp | 1ej3:A | 81.8 | 81 | 97 | 12 | 12 | 90 | 69 | 82.8 | 84 | 16 | 87 | 1.6 | 0.43 | 0.44 | 0.42 | 0.76 | 0.08 | 0.67 | 100.0 | 10.0 | 0.00 |
sec | 2000_05 | dssp | 1em2:A | 75.7 | 100 | 65 | 58 | 94 | 75 | 76 | 76.0 | 85 | 69 | 75 | 7.9 | 0.43 | 0.43 | 0.44 | 0.71 | 0.63 | 0.63 | 0.0 | 14.0 | 14.0 |
sec | 2000_05 | dssp | 1eo0:A | 67.5 | 75 | 76 | 0 | 0 | 50 | 60 | 75.4 | 83 | 100 | 57 | 6.4 | 0.11 | 0.13 | 0.10 | 0.25 | 1.0 | 0.36 | 0.0 | 1.0 | 6.0 |
sec | 2000_05 | dssp | 1eq6:A | 64.5 | 72 | 52 | 56 | 75 | 68 | 67 | 64.2 | 76 | 64 | 56 | 12.6 | 0.19 | 0.20 | 0.20 | 0.45 | 0.48 | 0.50 | 0.0 | 9.0 | 10.0 |
sec | 2000_05 | dssp | 1ewi:A | 57.9 | 69 | 21 | 75 | 70 | 49 | 85 | 53.1 | 40 | 75 | 48 | 4.3 | 0.22 | 0.25 | 0.20 | 0.24 | 0.63 | 0.34 | 0.0 | 25.0 | 1.0 |
sec | 2000_05 | dssp | THIS_month:psum | 72.6 | 81 | 68 | 41 | 53 | 68 | 75 | 73.1 | 79 | 67.2 | 68.1 | 4.3 | 0.31 | 0.32 | 0.31 | 0.54 | 0.62 | 0.54 | 57.1 | 9.8 | 4.9 |
sec | 2000_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 | 2000_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 | 2000_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) ) |