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_10 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_10 | 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_10 | 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_10 | 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_10 | dssp | THIS_month:psum | 67.7 | 62 | 60 | 45 | 48 | 64 | 67 | 64.9 | 62.5 | 67.5 | 60.9 | 5.6 | 0.22 | 0.22 | 0.22 | 0.51 | 0.61 | 0.42 | 68.7 | 9.8 | 7.1 |
sec | 2000_10 | dssp | 1c4r:A | 75.6 | 0 | 0 | 79 | 80 | 79 | 70 | 69.1 | 0 | 75 | 68 | 1.1 | 0.24 | 0.22 | 0.27 | 1.0 | 0.58 | 0.53 | 0.0 | 5.0 | 0.00 |
sec | 2000_10 | dssp | 1d6m:A | 62.0 | 75 | 66 | 40 | 80 | 52 | 50 | 58.4 | 66 | 53 | 43 | 4.8 | 0.16 | 0.16 | 0.18 | 0.37 | 0.51 | 0.26 | 100.0 | 6.0 | 8.0 |
sec | 2000_10 | dssp | 1d7b:A | 60.8 | 37 | 13 | 63 | 67 | 60 | 67 | 67.0 | 39 | 65 | 70 | 4.3 | 0.10 | 0.11 | 0.10 | 0.16 | 0.38 | 0.30 | 100.0 | 8.0 | 3.0 |
sec | 2000_10 | dssp | 1dl6:A | 72.4 | 0 | 0 | 75 | 30 | 72 | 94 | 63.9 | 100 | 42 | 66 | 0.0 | 0.11 | 0.14 | 0.09 | 1.0 | 0.34 | 0.34 | 100.0 | 0.00 | 20.0 |
sec | 2000_10 | dssp | 1e4f:T | 73.8 | 75 | 85 | 68 | 77 | 79 | 58 | 72.2 | 81 | 63 | 73 | 6.5 | 0.33 | 0.34 | 0.33 | 0.69 | 0.58 | 0.55 | 100.0 | 4.0 | 4.0 |
sec | 2000_10 | dssp | 1e68:A | 58.6 | 58 | 81 | 0 | 0 | 58 | 43 | 48.7 | 52 | 100 | 36 | 12.8 | 0.09 | 0.13 | 0.07 | 0.14 | 1.0 | 0.31 | 0.0 | 21.0 | 12.0 |
sec | 2000_10 | dssp | 1eg2:A | 72.6 | 69 | 73 | 55 | 89 | 84 | 67 | 67.4 | 71 | 60 | 68 | 3.3 | 0.31 | 0.30 | 0.32 | 0.57 | 0.64 | 0.53 | 0.0 | 1.0 | 8.0 |
sec | 2000_10 | dssp | 1ei5:A | 63.1 | 75 | 57 | 46 | 72 | 69 | 62 | 61.6 | 79 | 51 | 61 | 8.1 | 0.18 | 0.19 | 0.19 | 0.52 | 0.41 | 0.41 | 0.0 | 8.0 | 12.0 |
sec | 2000_10 | dssp | 1eje:A | 59.9 | 43 | 58 | 68 | 68 | 59 | 52 | 54.7 | 43 | 64 | 50 | 2.6 | 0.16 | 0.16 | 0.17 | 0.40 | 0.47 | 0.23 | 100.0 | 5.0 | 0.00 |
sec | 2000_10 | dssp | 1ev7:A | 47.4 | 39 | 62 | 42 | 28 | 58 | 49 | 45.2 | 45 | 25 | 53 | 13.6 | 0.04 | 0.04 | 0.04 | 0.23 | 0.16 | 0.20 | 100.0 | 16.0 | 8.0 |
sec | 2000_10 | dssp | 1ewq:A | 77.4 | 86 | 85 | 58 | 72 | 75 | 68 | 76.8 | 84 | 63 | 73 | 2.5 | 0.37 | 0.37 | 0.38 | 0.73 | 0.58 | 0.56 | 100.0 | 0.00 | 3.0 |
sec | 2000_10 | dssp | 1ezf:A | 66.1 | 71 | 84 | 0 | 0 | 51 | 44 | 52.5 | 58 | 100 | 38 | 3.7 | 0.07 | 0.08 | 0.06 | 0.31 | 1.0 | 0.26 | 0.0 | 11.0 | 6.0 |
sec | 2000_10 | dssp | 1f3u:A | 66.9 | 66 | 37 | 66 | 90 | 67 | 63 | 76.1 | 45 | 84 | 76 | 5.0 | 0.25 | 0.27 | 0.24 | 0.39 | 0.62 | 0.41 | 100.0 | 10.0 | 12.0 |
sec | 2000_10 | dssp | 1f3u:B | 48.4 | 45 | 23 | 40 | 83 | 57 | 51 | 45.9 | 16 | 56 | 47 | 11.2 | 0.10 | 0.10 | 0.10 | 0.11 | 0.42 | 0.18 | 100.0 | 16.0 | 20.0 |
sec | 2000_10 | dssp | 1f6u:A | 61.8 | 0 | 0 | 16 | 50 | 97 | 62 | 13.3 | 0 | 8 | 20 | 0.0 | 0.09 | 0.03 | 0.16 | 1.0 | 0.24 | 0.04 | 100.0 | 27.0 | 7.0 |
sec | 2000_10 | dssp | 1f81:A | 69.0 | 61 | 95 | 0 | 0 | 88 | 53 | 79.2 | 79 | 100 | 79 | 5.7 | 0.21 | 0.25 | 0.17 | 0.48 | 1.0 | 0.51 | 0.0 | 25.0 | 6.0 |
sec | 2000_10 | dssp | 1fft:C | 61.6 | 78 | 74 | 0 | 0 | 31 | 84 | 43.4 | 54 | 100 | 26 | 11.8 | 0.11 | 0.13 | 0.10 | 0.30 | 1.0 | 0.39 | 0.0 | 3.0 | 18.0 |
sec | 2000_10 | dssp | 1fho:A | 75.6 | 100 | 57 | 69 | 65 | 73 | 90 | 72.9 | 66 | 58 | 81 | 5.0 | 0.38 | 0.41 | 0.36 | 0.71 | 0.52 | 0.63 | 100.0 | 9.0 | 1.0 |
sec | 2000_10 | dssp | 1fio:A | 90.4 | 96 | 93 | 0 | 0 | 45 | 60 | 86.1 | 89 | 100 | 58 | 0.0 | 0.21 | 0.19 | 0.24 | 0.46 | 1.0 | 0.46 | 100.0 | 2.0 | 0.00 |
sec | 2000_10 | dssp | 1fiq:B | 63.0 | 82 | 54 | 55 | 68 | 51 | 73 | 64.5 | 70 | 69 | 57 | 8.5 | 0.21 | 0.21 | 0.22 | 0.44 | 0.51 | 0.41 | 0.0 | 17.0 | 4.0 |
sec | 2000_10 | dssp | 1fl4:A | 70.3 | 76 | 57 | 60 | 66 | 69 | 82 | 69.3 | 78 | 76 | 63 | 5.7 | 0.29 | 0.29 | 0.29 | 0.49 | 0.56 | 0.53 | 100.0 | 9.0 | 1.0 |
sec | 2000_10 | dssp | 1fnn:A | 76.4 | 84 | 81 | 70 | 66 | 66 | 71 | 79.7 | 85 | 74 | 73 | 1.9 | 0.31 | 0.32 | 0.32 | 0.62 | 0.64 | 0.52 | 100.0 | 1.0 | 0.00 |
sec | 2000_10 | dssp | 1fq0:A | 80.3 | 93 | 87 | 69 | 65 | 70 | 77 | 84.3 | 99 | 73 | 73 | 0.0 | 0.48 | 0.49 | 0.48 | 0.83 | 0.60 | 0.58 | 100.0 | 2.0 | 0.00 |
sec | 2000_10 | dssp | 1fqy:A | 56.6 | 50 | 82 | 0 | 0 | 66 | 76 | 68.7 | 65 | 100 | 73 | 22.5 | 0.18 | 0.23 | 0.14 | 0.33 | 1.0 | 0.55 | 0.0 | 23.0 | 28.0 |
sec | 2000_10 | dssp | 1ft9:A | 76.1 | 94 | 79 | 77 | 71 | 57 | 76 | 84.6 | 100 | 81 | 73 | 1.9 | 0.42 | 0.42 | 0.43 | 0.78 | 0.63 | 0.51 | 100.0 | 6.0 | 2.0 |
sec | 2000_10 | dssp | 1fu9:A | 55.6 | 100 | 40 | 0 | 0 | 45 | 90 | 60.6 | 88 | 0 | 59 | 8.3 | 0.18 | 0.15 | 0.21 | 0.41 | 1.0 | 0.40 | 100.0 | 41.0 | 11.0 |
sec | 2000_10 | dssp | 1fwq:A | 67.0 | 0 | 0 | 70 | 54 | 68 | 86 | 68.2 | 0 | 61 | 74 | 5.2 | 0.15 | 0.17 | 0.14 | -0.04 | 0.39 | 0.45 | 100.0 | 4.0 | 9.0 |
sec | 2000_10 | dssp | 1fxj:A | 71.3 | 85 | 78 | 64 | 69 | 65 | 67 | 71.9 | 85 | 64 | 67 | 1.5 | 0.33 | 0.34 | 0.34 | 0.73 | 0.53 | 0.43 | 0.0 | 2.0 | 1.0 |
sec | 2000_10 | dssp | 1gd2:E | 92.3 | 98 | 93 | 0 | 0 | 50 | 80 | 81.9 | 85 | 100 | 56 | 0.0 | 0.34 | 0.29 | 0.40 | 0.59 | 1.0 | 0.59 | 100.0 | 4.0 | 0.00 |
sec | 2000_10 | dssp | 1qmu:A | 75.5 | 67 | 93 | 71 | 67 | 82 | 72 | 72.3 | 69 | 78 | 70 | 2.3 | 0.37 | 0.36 | 0.38 | 0.73 | 0.58 | 0.56 | 100.0 | 7.0 | 1.0 |
sec | 2000_10 | dssp | 1qmy:A | 66.0 | 67 | 70 | 67 | 54 | 64 | 72 | 68.4 | 73 | 66 | 66 | 7.0 | 0.21 | 0.21 | 0.21 | 0.56 | 0.44 | 0.45 | 100.0 | 1.0 | 6.0 |
sec | 2000_10 | dssp | 1qnr:A | 53.8 | 31 | 75 | 63 | 31 | 69 | 62 | 50.9 | 36 | 53 | 60 | 14.8 | 0.10 | 0.10 | 0.10 | 0.33 | 0.27 | 0.37 | 100.0 | 22.0 | 18.0 |
sec | 2000_10 | dssp | THIS_month:psum | 67.7 | 62 | 60 | 45 | 48 | 64 | 67 | 64.9 | 62.5 | 67.5 | 60.9 | 5.6 | 0.22 | 0.22 | 0.22 | 0.51 | 0.61 | 0.42 | 68.7 | 9.8 | 7.1 |
sec | 2000_10 | 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_10 | 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_10 | 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) ) |