METHOD about: | ../../doc/explain_methods.html#PX_about_phd |
METHOD url: | PHD |
METHOD quote: | B Rost:: PHD: predicting one-dimensional protein structure by profile based neural networks. Methods in Enzymology, 266, 525-539, 1996. |
TYPE : | sec |
NPROT : | 1599 |
NWEEKS : | 109 |
AVE_Q3 : | 71.0 |
AVE_SOV: | 67.0 |
NOTE 1 : | here ALL results obtained for phd 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_10_07 | dssp | 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_10_07 | dssp | 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_10_07 | dssp | 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 |
Type | Method | Month | Nprot | Average Q3 for month | File with details for month |
---|---|---|---|---|---|
sec | phd | ALL | 1599 | 71.0 | |
sec | phd | 2000_04 | 10 | 72.1 | old/2000_04_phd.html |
sec | phd | 2000_05 | 15 | 72.7 | old/2000_05_phd.html |
sec | phd | 2000_06 | 10 | 72.9 | old/2000_06_phd.html |
sec | phd | 2000_07 | 28 | 70.7 | old/2000_07_phd.html |
sec | phd | 2000_08 | 18 | 74.9 | old/2000_08_phd.html |
sec | phd | 2000_09 | 24 | 73.3 | old/2000_09_phd.html |
sec | phd | 2000_10 | 33 | 67.7 | old/2000_10_phd.html |
sec | phd | 2000_11 | 33 | 71.0 | old/2000_11_phd.html |
sec | phd | 2000_12 | 38 | 73.6 | old/2000_12_phd.html |
sec | phd | 2001_01 | 24 | 74.4 | old/2001_01_phd.html |
sec | phd | 2001_02 | 28 | 69.6 | old/2001_02_phd.html |
sec | phd | 2001_03 | 36 | 70.9 | old/2001_03_phd.html |
sec | phd | 2001_04 | 11 | 68.4 | old/2001_04_phd.html |
sec | phd | 2001_05 | 12 | 71.8 | old/2001_05_phd.html |
sec | phd | 2001_06 | 16 | 65.7 | old/2001_06_phd.html |
sec | phd | 2001_07 | 25 | 70.1 | old/2001_07_phd.html |
sec | phd | 2001_08 | 46 | 69.8 | old/2001_08_phd.html |
sec | phd | 2001_09 | 35 | 70.7 | old/2001_09_phd.html |
sec | phd | 2001_10 | 7 | 60.0 | old/2001_10_phd.html |
sec | phd | 2001_11 | 15 | 77.0 | old/2001_11_phd.html |
sec | phd | 2001_12 | 147 | 67.1 | old/2001_12_phd.html |
sec | phd | 2002_01 | 37 | 67.9 | old/2002_01_phd.html |
sec | phd | 2002_02 | 30 | 65.5 | old/2002_02_phd.html |
sec | phd | 2002_03 | 27 | 72.0 | old/2002_03_phd.html |
sec | phd | 2002_04 | 23 | 70.8 | old/2002_04_phd.html |
sec | phd | 2002_05 | 39 | 66.9 | old/2002_05_phd.html |
sec | phd | 2002_06 | 21 | 67.2 | old/2002_06_phd.html |
sec | phd | 2002_07 | 23 | 76.4 | old/2002_07_phd.html |
sec | phd | ALL | 1599 | 71.0 |
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) ) |