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_02 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_02 | 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_02 | 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_02 | 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_02 | dssp | THIS_month:psum | 65.4 | 55 | 58 | 42 | 43 | 66 | 68 | 62.9 | 62.1 | 67.9 | 60.1 | 5.7 | 0.23 | 0.23 | 0.23 | 0.51 | 0.53 | 0.40 | 82.7 | 9.3 | 7.3 |
sec | 2002_02 | dssp | 1eq1:A | 80.1 | 96 | 80 | 0 | 0 | 34 | 78 | 55.3 | 57 | 100 | 48 | 0.0 | 0.18 | 0.14 | 0.22 | 0.42 | 1.0 | 0.42 | 100.0 | 15.0 | 0.00 |
sec | 2002_02 | dssp | 1g9p:A | 60.0 | 0 | 0 | 55 | 45 | 66 | 75 | 34.5 | 0 | 47 | 34 | 0.0 | 0.12 | 0.14 | 0.11 | -0.09 | 0.36 | 0.07 | 100.0 | 4.0 | 4.0 |
sec | 2002_02 | dssp | 1h67:A | 69.4 | 73 | 85 | 0 | 0 | 61 | 60 | 62.8 | 83 | 100 | 39 | 1.8 | 0.17 | 0.20 | 0.14 | 0.49 | 1.0 | 0.38 | 0.0 | 8.0 | 7.0 |
sec | 2002_02 | dssp | 1i2v:A | 54.5 | 0 | 0 | 91 | 40 | 52 | 76 | 52.5 | 0 | 67 | 60 | 9.0 | 0.11 | 0.09 | 0.13 | 1.0 | 0.38 | 0.31 | 100.0 | 15.0 | 34.0 |
sec | 2002_02 | dssp | 1igq:D | 35.6 | 0 | 0 | 22 | 100 | 56 | 70 | 40.2 | 0 | 22 | 66 | 35.5 | 0.25 | 0.27 | 0.24 | -0.25 | 0.34 | 0.40 | 100.0 | 49.0 | 40.0 |
sec | 2002_02 | dssp | 1itp:A | 64.9 | 91 | 77 | 34 | 60 | 71 | 57 | 65.5 | 100 | 38 | 62 | 5.1 | 0.32 | 0.31 | 0.33 | 0.76 | 0.27 | 0.39 | 100.0 | 5.0 | 14.0 |
sec | 2002_02 | dssp | 1j7x:A | 72.8 | 78 | 76 | 75 | 63 | 66 | 74 | 77.4 | 89 | 77 | 68 | 2.9 | 0.32 | 0.33 | 0.32 | 0.64 | 0.60 | 0.50 | 0.0 | 0.00 | 3.0 |
sec | 2002_02 | dssp | 1jdq:A | 81.6 | 72 | 88 | 90 | 71 | 81 | 84 | 93.2 | 90 | 93 | 94 | 0.0 | 0.48 | 0.49 | 0.49 | 0.75 | 0.74 | 0.63 | 100.0 | 4.0 | 6.0 |
sec | 2002_02 | dssp | 1jeo:A | 71.8 | 81 | 78 | 62 | 53 | 59 | 68 | 77.3 | 90 | 59 | 63 | 5.6 | 0.24 | 0.24 | 0.24 | 0.56 | 0.50 | 0.47 | 100.0 | 2.0 | 2.0 |
sec | 2002_02 | dssp | 1jkz:A | 34.8 | 0 | 0 | 43 | 41 | 47 | 31 | 40.2 | 0 | 62 | 44 | 0.0 | 0.16 | 0.12 | 0.20 | 1.0 | 0.10 | -0.27 | 100.0 | 23.0 | 2.0 |
sec | 2002_02 | dssp | 1jmu:B | 64.8 | 72 | 87 | 50 | 42 | 63 | 57 | 48.6 | 55 | 54 | 40 | 0.0 | 0.30 | 0.31 | 0.30 | 0.67 | 0.34 | 0.28 | 100.0 | 7.0 | 2.0 |
sec | 2002_02 | dssp | 1jnr:B | 74.5 | 40 | 53 | 80 | 65 | 79 | 82 | 75.2 | 35 | 84 | 80 | 2.0 | 0.26 | 0.26 | 0.27 | 0.39 | 0.62 | 0.50 | 100.0 | 3.0 | 5.0 |
sec | 2002_02 | dssp | 1jrm:A | 71.2 | 70 | 84 | 63 | 56 | 74 | 71 | 65.1 | 90 | 81 | 52 | 1.9 | 0.32 | 0.33 | 0.33 | 0.69 | 0.47 | 0.46 | 100.0 | 4.0 | 2.0 |
sec | 2002_02 | dssp | 1jsb:A | 54.3 | 62 | 62 | 63 | 42 | 47 | 65 | 55.0 | 81 | 58 | 47 | 1.4 | 0.16 | 0.16 | 0.16 | 0.57 | 0.22 | 0.14 | 100.0 | 0.00 | 15.0 |
sec | 2002_02 | dssp | 1jw2:A | 86.1 | 89 | 89 | 0 | 0 | 79 | 79 | 93.1 | 100 | 100 | 79 | 0.0 | 0.38 | 0.38 | 0.38 | 0.68 | 1.0 | 0.68 | 100.0 | 0.00 | 0.00 |
sec | 2002_02 | dssp | 1jw3:A | 55.0 | 90 | 51 | 44 | 52 | 44 | 61 | 60.5 | 100 | 48 | 49 | 8.5 | 0.18 | 0.19 | 0.18 | 0.56 | 0.25 | 0.24 | 0.0 | 17.0 | 4.0 |
sec | 2002_02 | dssp | 1jy1:A | 58.0 | 72 | 50 | 39 | 64 | 58 | 63 | 55.7 | 65 | 43 | 56 | 7.0 | 0.13 | 0.13 | 0.14 | 0.39 | 0.39 | 0.29 | 100.0 | 13.0 | 9.0 |
sec | 2002_02 | dssp | 1jyg:A | 56.5 | 45 | 80 | 0 | 0 | 76 | 48 | 49.9 | 45 | 100 | 59 | 5.7 | 0.06 | 0.07 | 0.05 | 0.25 | 1.0 | 0.29 | 0.0 | 27.0 | 7.0 |
sec | 2002_02 | dssp | 1k0s:A | 65.6 | 57 | 20 | 63 | 74 | 68 | 87 | 70.0 | 59 | 72 | 69 | 14.5 | 0.25 | 0.27 | 0.23 | 0.22 | 0.48 | 0.61 | 100.0 | 16.0 | 5.0 |
sec | 2002_02 | dssp | 1k1f:A | 88.1 | 87 | 100 | 0 | 0 | 89 | 73 | 85.6 | 97 | 100 | 67 | 0.0 | 0.59 | 0.67 | 0.52 | 0.81 | 1.0 | 0.73 | 100.0 | 8.0 | 2.0 |
sec | 2002_02 | dssp | 1k28:D | 66.4 | 61 | 55 | 58 | 68 | 74 | 70 | 58.8 | 59 | 59 | 58 | 7.8 | 0.19 | 0.19 | 0.19 | 0.47 | 0.45 | 0.48 | 100.0 | 2.0 | 5.0 |
sec | 2002_02 | dssp | 1k6w:A | 68.3 | 72 | 71 | 60 | 64 | 68 | 67 | 65.4 | 71 | 69 | 58 | 5.4 | 0.22 | 0.23 | 0.23 | 0.55 | 0.51 | 0.45 | 100.0 | 0.00 | 1.0 |
sec | 2002_02 | dssp | 1kbh:A | 83.0 | 79 | 92 | 0 | 0 | 88 | 72 | 86.1 | 86 | 100 | 85 | 0.0 | 0.35 | 0.36 | 0.35 | 0.66 | 1.0 | 0.66 | 100.0 | 8.0 | 0.00 |
sec | 2002_02 | dssp | 1khc:A | 63.0 | 59 | 57 | 37 | 83 | 78 | 63 | 62.1 | 63 | 40 | 71 | 9.6 | 0.18 | 0.18 | 0.20 | 0.31 | 0.49 | 0.46 | 100.0 | 1.0 | 11.0 |
sec | 2002_02 | dssp | 1kps:B | 66.7 | 70 | 78 | 0 | 0 | 60 | 77 | 60.1 | 74 | 100 | 44 | 12.1 | 0.18 | 0.22 | 0.15 | 0.36 | 1.0 | 0.53 | 0.0 | 6.0 | 14.0 |
sec | 2002_02 | dssp | 1kq4:C | 57.6 | 33 | 100 | 61 | 50 | 72 | 57 | 67.0 | 44 | 76 | 73 | 15.1 | 0.21 | 0.20 | 0.23 | 0.51 | 0.21 | 0.43 | 100.0 | 18.0 | 9.0 |
sec | 2002_02 | dssp | 1kqi:A | 60.5 | 0 | 0 | 30 | 33 | 71 | 76 | 39.9 | 100 | 13 | 49 | 2.6 | 0.00 | 0.01 | 0.01 | 1.0 | 0.08 | 0.10 | 100.0 | 7.0 | 2.0 |
sec | 2002_02 | dssp | 1ktz:B | 65.1 | 0 | 0 | 58 | 66 | 74 | 73 | 66.0 | 0 | 62 | 72 | 7.5 | 0.20 | 0.21 | 0.19 | -0.04 | 0.34 | 0.45 | 100.0 | 4.0 | 5.0 |
sec | 2002_02 | dssp | 1kwh:A | 68.3 | 71 | 83 | 50 | 37 | 71 | 68 | 62.3 | 70 | 47 | 59 | 7.1 | 0.22 | 0.23 | 0.22 | 0.60 | 0.32 | 0.49 | 100.0 | 6.0 | 4.0 |
sec | 2002_02 | dssp | THIS_month:psum | 65.4 | 55 | 58 | 42 | 43 | 66 | 68 | 62.9 | 62.1 | 67.9 | 60.1 | 5.7 | 0.23 | 0.23 | 0.23 | 0.51 | 0.53 | 0.40 | 82.7 | 9.3 | 7.3 |
sec | 2002_02 | 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_02 | 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_02 | 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) ) |