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_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 | 2001_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 | 2001_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 | 2001_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 | 2001_01 | dssp | THIS_month:psum | 74.3 | 67 | 70 | 40 | 44 | 73 | 65 | 71.6 | 76.2 | 69.6 | 62.3 | 2.2 | 0.29 | 0.30 | 0.28 | 0.62 | 0.60 | 0.44 | 82.6 | 7.0 | 4.5 |
sec | 2001_01 | dssp | 1dqe:A | 77.4 | 85 | 83 | 0 | 0 | 66 | 70 | 77.0 | 90 | 0 | 62 | 0.0 | 0.26 | 0.27 | 0.27 | 0.59 | -0.01 | 0.51 | 100.0 | 1.0 | 0.00 |
sec | 2001_01 | dssp | 1emx:A | 70.0 | 0 | 0 | 0 | 0 | 75 | 91 | 70.0 | 100 | 0 | 75 | 0.0 | 0.05 | 0.07 | 0.03 | 1.0 | -0.14 | -0.14 | 100.0 | 0.00 | 16.0 |
sec | 2001_01 | dssp | 1ep1:B | 62.8 | 88 | 48 | 45 | 81 | 66 | 65 | 60.7 | 86 | 55 | 54 | 6.5 | 0.22 | 0.22 | 0.22 | 0.54 | 0.46 | 0.38 | 100.0 | 15.0 | 16.0 |
sec | 2001_01 | dssp | 1es8:A | 64.9 | 76 | 81 | 58 | 87 | 50 | 30 | 51.4 | 47 | 75 | 28 | 0.0 | 0.35 | 0.36 | 0.36 | 0.61 | 0.61 | 0.16 | 100.0 | 2.0 | 10.0 |
sec | 2001_01 | dssp | 1f9a:A | 75.6 | 73 | 87 | 62 | 50 | 82 | 76 | 78.3 | 80 | 72 | 78 | 6.7 | 0.33 | 0.34 | 0.33 | 0.66 | 0.47 | 0.63 | 100.0 | 6.0 | 3.0 |
sec | 2001_01 | dssp | 1fc6:A | 77.7 | 86 | 80 | 71 | 81 | 75 | 74 | 78.6 | 88 | 78 | 72 | 0.2 | 0.43 | 0.43 | 0.43 | 0.76 | 0.68 | 0.55 | 0.0 | 2.0 | 3.0 |
sec | 2001_01 | dssp | 1fe6:A | 73.1 | 71 | 100 | 0 | 0 | 100 | 23 | 96.8 | 100 | 100 | 45 | 7.6 | 0.24 | 0.39 | 0.10 | 0.35 | 1.0 | 0.42 | 100.0 | 26.0 | 7.0 |
sec | 2001_01 | dssp | 1fh1:A | 64.7 | 90 | 66 | 0 | 0 | 16 | 50 | 63.6 | 93 | 100 | 8 | 0.0 | 0.01 | 0.01 | 0.02 | 0.11 | 1.0 | 0.11 | 100.0 | 23.0 | 0.00 |
sec | 2001_01 | dssp | 1fm0:D | 76.5 | 91 | 61 | 59 | 100 | 77 | 82 | 73.4 | 92 | 63 | 67 | 6.1 | 0.42 | 0.41 | 0.43 | 0.62 | 0.71 | 0.64 | 100.0 | 13.0 | 11.0 |
sec | 2001_01 | dssp | 1fm0:E | 84.6 | 100 | 88 | 85 | 80 | 76 | 86 | 92.3 | 100 | 100 | 82 | 0.0 | 0.59 | 0.60 | 0.59 | 0.92 | 0.72 | 0.68 | 100.0 | 2.0 | 2.0 |
sec | 2001_01 | dssp | 1foe:A | 81.0 | 86 | 86 | 80 | 74 | 72 | 74 | 73.4 | 79 | 77 | 64 | 2.1 | 0.40 | 0.41 | 0.41 | 0.69 | 0.73 | 0.61 | 100.0 | 0.00 | 1.0 |
sec | 2001_01 | dssp | 1fqt:A | 78.0 | 0 | 0 | 70 | 82 | 87 | 75 | 74.7 | 0 | 82 | 71 | 0.0 | 0.27 | 0.25 | 0.30 | 1.0 | 0.60 | 0.56 | 100.0 | 2.0 | 6.0 |
sec | 2001_01 | dssp | 1fy2:A | 78.1 | 81 | 89 | 82 | 60 | 74 | 79 | 76.5 | 90 | 80 | 67 | 0.0 | 0.45 | 0.46 | 0.44 | 0.78 | 0.63 | 0.56 | 100.0 | 3.0 | 6.0 |
sec | 2001_01 | dssp | 1fzp:D | 67.9 | 71 | 80 | 0 | 0 | 58 | 47 | 77.7 | 85 | 100 | 59 | 0.0 | 0.06 | 0.07 | 0.06 | 0.29 | 1.0 | 0.29 | 100.0 | 7.0 | 0.00 |
sec | 2001_01 | dssp | 1fzr:A | 51.9 | 17 | 53 | 60 | 56 | 72 | 49 | 46.6 | 25 | 59 | 54 | 5.4 | 0.10 | 0.10 | 0.12 | 0.16 | 0.42 | 0.19 | 0.0 | 20.0 | 1.0 |
sec | 2001_01 | dssp | 1g1i:A | 95.3 | 94 | 100 | 0 | 0 | 100 | 71 | 98.4 | 100 | 100 | 86 | 0.0 | 0.65 | 0.73 | 0.59 | 0.82 | 1.0 | 0.82 | 100.0 | 4.0 | 0.00 |
sec | 2001_01 | dssp | 1g2c:A | 90.0 | 93 | 95 | 0 | 0 | 50 | 40 | 63.0 | 64 | 100 | 33 | 0.0 | 0.15 | 0.17 | 0.15 | 0.39 | 1.0 | 0.39 | 100.0 | 2.0 | 0.00 |
sec | 2001_01 | dssp | 1g2c:B | 90.0 | 93 | 93 | 0 | 0 | 81 | 81 | 68.8 | 62 | 100 | 100 | 0.0 | 0.46 | 0.47 | 0.47 | 0.74 | 1.0 | 0.74 | 100.0 | 0.00 | 0.00 |
sec | 2001_01 | dssp | 1g4u:S | 77.5 | 88 | 90 | 38 | 62 | 81 | 67 | 73.8 | 84 | 43 | 73 | 1.1 | 0.43 | 0.41 | 0.45 | 0.81 | 0.41 | 0.56 | 100.0 | 1.0 | 6.0 |
sec | 2001_01 | dssp | 1g55:A | 70.5 | 55 | 80 | 68 | 72 | 86 | 65 | 66.9 | 65 | 73 | 63 | 6.4 | 0.34 | 0.33 | 0.35 | 0.52 | 0.61 | 0.55 | 0.0 | 11.0 | 1.0 |
sec | 2001_01 | dssp | 1g6o:A | 70.0 | 62 | 81 | 66 | 79 | 79 | 60 | 71.3 | 76 | 77 | 63 | 1.2 | 0.31 | 0.30 | 0.32 | 0.56 | 0.66 | 0.44 | 0.0 | 9.0 | 3.0 |
sec | 2001_01 | dssp | 1g73:C | 59.6 | 47 | 72 | 55 | 27 | 71 | 65 | 59.1 | 48 | 42 | 72 | 8.9 | 0.13 | 0.14 | 0.13 | 0.37 | 0.29 | 0.37 | 100.0 | 14.0 | 10.0 |
sec | 2001_01 | dssp | 1hx2:A | 73.3 | 0 | 0 | 25 | 30 | 85 | 82 | 54.8 | 100 | 27 | 59 | 0.0 | 0.01 | 0.01 | 0.01 | 1.0 | 0.11 | 0.11 | 100.0 | 0.00 | 3.0 |
sec | 2001_01 | dssp | THIS_month:psum | 74.3 | 67 | 70 | 40 | 44 | 73 | 65 | 71.6 | 76.2 | 69.6 | 62.3 | 2.2 | 0.29 | 0.30 | 0.28 | 0.62 | 0.60 | 0.44 | 82.6 | 7.0 | 4.5 |
sec | 2001_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 | 2001_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 | 2001_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) ) |